gromacs →
2020.6-2 →
armhf → 2021-04-18 15:48:20
sbuild (Debian sbuild) 0.71.0 (24 Aug 2016) on testwandboard
+==============================================================================+
| gromacs 2020.6-2 (armhf) Sun, 18 Apr 2021 05:25:04 +0000 |
+==============================================================================+
Package: gromacs
Version: 2020.6-2
Source Version: 2020.6-2
Distribution: bullseye-staging
Machine Architecture: armhf
Host Architecture: armhf
Build Architecture: armhf
I: NOTICE: Log filtering will replace 'var/lib/schroot/mount/bullseye-staging-armhf-sbuild-5e2b5fa6-7c6d-42dc-9882-dae9be53cd7f' with '<<CHROOT>>'
+------------------------------------------------------------------------------+
| Update chroot |
+------------------------------------------------------------------------------+
Get:1 http://172.17.0.1/private bullseye-staging InRelease [11.3 kB]
Get:2 http://172.17.0.1/private bullseye-staging/main Sources [12.2 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf Packages [13.2 MB]
Fetched 25.5 MB in 31s (815 kB/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Fetch source files |
+------------------------------------------------------------------------------+
Check APT
---------
Checking available source versions...
Download source files with APT
------------------------------
Reading package lists...
NOTICE: 'gromacs' packaging is maintained in the 'Git' version control system at:
https://salsa.debian.org/debichem-team/gromacs.git
Please use:
git clone https://salsa.debian.org/debichem-team/gromacs.git
to retrieve the latest (possibly unreleased) updates to the package.
Need to get 77.8 MB of source archives.
Get:1 http://172.17.0.1/private bullseye-staging/main gromacs 2020.6-2 (dsc) [2948 B]
Get:2 http://172.17.0.1/private bullseye-staging/main gromacs 2020.6-2 (tar) [48.5 MB]
Get:3 http://172.17.0.1/private bullseye-staging/main gromacs 2020.6-2 (tar) [29.2 MB]
Get:4 http://172.17.0.1/private bullseye-staging/main gromacs 2020.6-2 (diff) [38.3 kB]
Fetched 77.8 MB in 30s (2620 kB/s)
Download complete and in download only mode
I: NOTICE: Log filtering will replace 'build/gromacs-mFqGjY/gromacs-2020.6' with '<<PKGBUILDDIR>>'
I: NOTICE: Log filtering will replace 'build/gromacs-mFqGjY' with '<<BUILDDIR>>'
+------------------------------------------------------------------------------+
| Install build-essential |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: build-essential, fakeroot
Filtered Build-Depends: build-essential, fakeroot
dpkg-deb: building package 'sbuild-build-depends-core-dummy' in '/<<BUILDDIR>>/resolver-yIzPYi/apt_archive/sbuild-build-depends-core-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy
dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
gpg: keybox '/<<BUILDDIR>>/resolver-yIzPYi/gpg/pubring.kbx' created
gpg: /<<BUILDDIR>>/resolver-yIzPYi/gpg/trustdb.gpg: trustdb created
gpg: key 35506D9A48F77B2E: public key "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" imported
gpg: Total number processed: 1
gpg: imported: 1
gpg: key 35506D9A48F77B2E: "Sbuild Signer (Sbuild Build Dependency Archive Key) <buildd-tools-devel@lists.alioth.debian.org>" not changed
gpg: key 35506D9A48F77B2E: secret key imported
gpg: Total number processed: 1
gpg: unchanged: 1
gpg: secret keys read: 1
gpg: secret keys imported: 1
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ Release [957 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ Sources [349 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ Packages [429 B]
Fetched 2105 B in 1s (2808 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install core build dependencies (apt-based resolver)
----------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
bsdextrautils libnss-nis libnss-nisplus libpam-cap netbase sensible-utils
Use 'apt autoremove' to remove them.
The following NEW packages will be installed:
sbuild-build-depends-core-dummy
0 upgraded, 1 newly installed, 0 to remove and 13 not upgraded.
Need to get 852 B of archives.
After this operation, 0 B of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ sbuild-build-depends-core-dummy 0.invalid.0 [852 B]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 852 B in 0s (23.0 kB/s)
Selecting previously unselected package sbuild-build-depends-core-dummy.
(Reading database ... 12579 files and directories currently installed.)
Preparing to unpack .../sbuild-build-depends-core-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-core-dummy (0.invalid.0) ...
Setting up sbuild-build-depends-core-dummy (0.invalid.0) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Check architectures |
+------------------------------------------------------------------------------+
Arch check ok (armhf included in any all)
+------------------------------------------------------------------------------+
| Install package build dependencies |
+------------------------------------------------------------------------------+
Setup apt archive
-----------------
Merged Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.4-5), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
Filtered Build-Depends: chrpath, cmake, debhelper-compat (= 13), libblas-dev, libboost-dev, libfftw3-dev, liblapack-dev, libmpich-dev (>= 3.4-5), libopenmpi-dev (>= 1.10.2-7), libx11-dev, lsb-release, mpich, openmpi-bin, zlib1g-dev
dpkg-deb: building package 'sbuild-build-depends-gromacs-dummy' in '/<<BUILDDIR>>/resolver-yIzPYi/apt_archive/sbuild-build-depends-gromacs-dummy.deb'.
dpkg-scanpackages: warning: Packages in archive but missing from override file:
dpkg-scanpackages: warning: sbuild-build-depends-core-dummy sbuild-build-depends-gromacs-dummy
dpkg-scanpackages: info: Wrote 2 entries to output Packages file.
gpg: using "Sbuild Signer" as default secret key for signing
Ign:1 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ InRelease
Get:2 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ Release [963 B]
Get:3 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ Release.gpg [370 B]
Get:4 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ Sources [585 B]
Get:5 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ Packages [667 B]
Fetched 2585 B in 1s (3406 B/s)
Reading package lists...
W: No sandbox user '_apt' on the system, can not drop privileges
Reading package lists...
Install gromacs build dependencies (apt-based resolver)
-------------------------------------------------------
Installing build dependencies
Reading package lists...
Building dependency tree...
Reading state information...
The following packages were automatically installed and are no longer required:
libnss-nis libnss-nisplus libpam-cap netbase
Use 'apt autoremove' to remove them.
The following additional packages will be installed:
autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext
gettext-base gfortran gfortran-10 groff-base hwloc-nox ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgfortran-10-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67
libjs-jquery libjs-jquery-ui libjsoncpp24 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3 libmpich-dev
libmpich12 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8
libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libslurm36
libssh2-1 libsub-override-perl libtool libuchardet0 libuv1 libx11-6
libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev
libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db media-types
mpich ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
po-debconf procps python3 python3-minimal python3.9 python3.9-minimal
x11proto-dev xorg-sgml-doctools xtrans-dev zlib1g-dev
Suggested packages:
autoconf-archive gnu-standards autoconf-doc cmake-doc ninja-build dh-make
gettext-doc libasprintf-dev libgettextpo-dev gfortran-doc gfortran-10-doc
libcoarrays-dev groff lrzip liblapack-doc libboost-doc libboost1.74-doc
libboost-atomic1.74-dev libboost-chrono1.74-dev libboost-container1.74-dev
libboost-context1.74-dev libboost-contract1.74-dev
libboost-coroutine1.74-dev libboost-date-time1.74-dev
libboost-exception1.74-dev libboost-fiber1.74-dev
libboost-filesystem1.74-dev libboost-graph1.74-dev
libboost-graph-parallel1.74-dev libboost-iostreams1.74-dev
libboost-locale1.74-dev libboost-log1.74-dev libboost-math1.74-dev
libboost-mpi1.74-dev libboost-mpi-python1.74-dev libboost-numpy1.74-dev
libboost-program-options1.74-dev libboost-python1.74-dev
libboost-random1.74-dev libboost-regex1.74-dev
libboost-serialization1.74-dev libboost-stacktrace1.74-dev
libboost-system1.74-dev libboost-test1.74-dev libboost-thread1.74-dev
libboost-timer1.74-dev libboost-type-erasure1.74-dev libboost-wave1.74-dev
libboost1.74-tools-dev libmpfrc++-dev libntl-dev libboost-nowide1.74-dev
libfftw3-doc libjs-jquery-ui-docs libtool-doc openmpi-doc pciutils gcj-jdk
libx11-doc libxcb-doc m4-doc apparmor less www-browser mpich-doc opencl-icd
keychain libpam-ssh monkeysphere ssh-askpass libmail-box-perl python3-doc
python3-tk python3-venv python3.9-venv python3.9-doc binfmt-support
Recommended packages:
curl | wget | lynx ca-certificates libarchive-cpio-perl javascript-common
libgpm2 libcoarrays-openmpi-dev publicsuffix xauth libmail-sendmail-perl
psmisc
The following NEW packages will be installed:
autoconf automake autopoint autotools-dev chrpath cmake cmake-data debhelper
dh-autoreconf dh-strip-nondeterminism distro-info-data dwz file gettext
gettext-base gfortran gfortran-10 groff-base hwloc-nox ibverbs-providers
intltool-debian libarchive-zip-perl libarchive13 libblas-dev libblas3
libboost-dev libboost1.74-dev libbrotli1 libbsd0 libcbor0 libcurl4
libdebhelper-perl libedit2 libelf1 libevent-2.1-7 libevent-core-2.1-7
libevent-dev libevent-extra-2.1-7 libevent-openssl-2.1-7
libevent-pthreads-2.1-7 libexpat1 libfabric1 libfftw3-bin libfftw3-dev
libfftw3-double3 libfftw3-single3 libfido2-1
libfile-stripnondeterminism-perl libgfortran-10-dev libgfortran5
libhwloc-dev libhwloc-plugins libhwloc15 libibverbs-dev libibverbs1 libicu67
libjs-jquery libjs-jquery-ui libjsoncpp24 liblapack-dev liblapack3
libltdl-dev libltdl7 libmagic-mgc libmagic1 libmd0 libmpdec3 libmpich-dev
libmpich12 libncurses6 libnghttp2-14 libnl-3-200 libnl-3-dev
libnl-route-3-200 libnl-route-3-dev libnuma-dev libnuma1 libopenmpi-dev
libopenmpi3 libpciaccess0 libpipeline1 libpmix-dev libpmix2 libprocps8
libpsl5 libpthread-stubs0-dev libpython3-stdlib libpython3.9-minimal
libpython3.9-stdlib librdmacm1 librhash0 librtmp1 libsigsegv2 libslurm36
libssh2-1 libsub-override-perl libtool libuchardet0 libuv1 libx11-6
libx11-data libx11-dev libxau-dev libxau6 libxcb1 libxcb1-dev libxdmcp-dev
libxdmcp6 libxext6 libxml2 libxnvctrl0 lsb-release m4 man-db media-types
mpich ocl-icd-libopencl1 openmpi-bin openmpi-common openssh-client
po-debconf procps python3 python3-minimal python3.9 python3.9-minimal
sbuild-build-depends-gromacs-dummy x11proto-dev xorg-sgml-doctools
xtrans-dev zlib1g-dev
0 upgraded, 131 newly installed, 0 to remove and 13 not upgraded.
Need to get 69.8 MB of archives.
After this operation, 392 MB of additional disk space will be used.
Get:1 copy:/<<BUILDDIR>>/resolver-yIzPYi/apt_archive ./ sbuild-build-depends-gromacs-dummy 0.invalid.0 [952 B]
Get:2 http://172.17.0.1/private bullseye-staging/main armhf libuchardet0 armhf 0.0.7-1 [65.0 kB]
Get:3 http://172.17.0.1/private bullseye-staging/main armhf groff-base armhf 1.22.4-6 [793 kB]
Get:4 http://172.17.0.1/private bullseye-staging/main armhf libpipeline1 armhf 1.5.3-1 [29.9 kB]
Get:5 http://172.17.0.1/private bullseye-staging/main armhf man-db armhf 2.9.4-2 [1307 kB]
Get:6 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-minimal armhf 3.9.2-1+rpi1 [791 kB]
Get:7 http://172.17.0.1/private bullseye-staging/main armhf libexpat1 armhf 2.2.10-2 [73.4 kB]
Get:8 http://172.17.0.1/private bullseye-staging/main armhf python3.9-minimal armhf 3.9.2-1+rpi1 [1625 kB]
Get:9 http://172.17.0.1/private bullseye-staging/main armhf python3-minimal armhf 3.9.2-2 [38.2 kB]
Get:10 http://172.17.0.1/private bullseye-staging/main armhf media-types all 4.0.0 [30.3 kB]
Get:11 http://172.17.0.1/private bullseye-staging/main armhf libmpdec3 armhf 2.5.1-1+rpi1 [73.4 kB]
Get:12 http://172.17.0.1/private bullseye-staging/main armhf libpython3.9-stdlib armhf 3.9.2-1+rpi1 [1616 kB]
Get:13 http://172.17.0.1/private bullseye-staging/main armhf python3.9 armhf 3.9.2-1+rpi1 [466 kB]
Get:14 http://172.17.0.1/private bullseye-staging/main armhf libpython3-stdlib armhf 3.9.2-2 [21.3 kB]
Get:15 http://172.17.0.1/private bullseye-staging/main armhf python3 armhf 3.9.2-2 [37.8 kB]
Get:16 http://172.17.0.1/private bullseye-staging/main armhf libncurses6 armhf 6.2+20201114-2 [79.9 kB]
Get:17 http://172.17.0.1/private bullseye-staging/main armhf libprocps8 armhf 2:3.3.17-5 [60.5 kB]
Get:18 http://172.17.0.1/private bullseye-staging/main armhf procps armhf 2:3.3.17-5 [475 kB]
Get:19 http://172.17.0.1/private bullseye-staging/main armhf libmagic-mgc armhf 1:5.39-3 [273 kB]
Get:20 http://172.17.0.1/private bullseye-staging/main armhf libmagic1 armhf 1:5.39-3 [117 kB]
Get:21 http://172.17.0.1/private bullseye-staging/main armhf file armhf 1:5.39-3 [68.0 kB]
Get:22 http://172.17.0.1/private bullseye-staging/main armhf gettext-base armhf 0.21-4 [171 kB]
Get:23 http://172.17.0.1/private bullseye-staging/main armhf libmd0 armhf 1.0.3-3 [27.2 kB]
Get:24 http://172.17.0.1/private bullseye-staging/main armhf libbsd0 armhf 0.11.3-1 [103 kB]
Get:25 http://172.17.0.1/private bullseye-staging/main armhf libedit2 armhf 3.1-20191231-2 [80.2 kB]
Get:26 http://172.17.0.1/private bullseye-staging/main armhf libcbor0 armhf 0.5.0+dfsg-2 [19.5 kB]
Get:27 http://172.17.0.1/private bullseye-staging/main armhf libfido2-1 armhf 1.6.0-2 [47.2 kB]
Get:28 http://172.17.0.1/private bullseye-staging/main armhf openssh-client armhf 1:8.4p1-5 [793 kB]
Get:29 http://172.17.0.1/private bullseye-staging/main armhf libsigsegv2 armhf 2.13-1 [34.3 kB]
Get:30 http://172.17.0.1/private bullseye-staging/main armhf m4 armhf 1.4.18-5 [186 kB]
Get:31 http://172.17.0.1/private bullseye-staging/main armhf autoconf all 2.69-14 [313 kB]
Get:32 http://172.17.0.1/private bullseye-staging/main armhf autotools-dev all 20180224.1+nmu1 [77.1 kB]
Get:33 http://172.17.0.1/private bullseye-staging/main armhf automake all 1:1.16.3-2 [814 kB]
Get:34 http://172.17.0.1/private bullseye-staging/main armhf autopoint all 0.21-4 [510 kB]
Get:35 http://172.17.0.1/private bullseye-staging/main armhf chrpath armhf 0.16-2 [15.4 kB]
Get:36 http://172.17.0.1/private bullseye-staging/main armhf cmake-data all 3.18.4-2+rpi1 [1725 kB]
Get:37 http://172.17.0.1/private bullseye-staging/main armhf libicu67 armhf 67.1-6 [8289 kB]
Get:38 http://172.17.0.1/private bullseye-staging/main armhf libxml2 armhf 2.9.10+dfsg-6.3 [580 kB]
Get:39 http://172.17.0.1/private bullseye-staging/main armhf libarchive13 armhf 3.4.3-2 [294 kB]
Get:40 http://172.17.0.1/private bullseye-staging/main armhf libbrotli1 armhf 1.0.9-2+b1 [261 kB]
Get:41 http://172.17.0.1/private bullseye-staging/main armhf libnghttp2-14 armhf 1.43.0-1 [65.3 kB]
Get:42 http://172.17.0.1/private bullseye-staging/main armhf libpsl5 armhf 0.21.0-1.2 [56.2 kB]
Get:43 http://172.17.0.1/private bullseye-staging/main armhf librtmp1 armhf 2.4+20151223.gitfa8646d.1-2+b2 [54.2 kB]
Get:44 http://172.17.0.1/private bullseye-staging/main armhf libssh2-1 armhf 1.9.0-2 [141 kB]
Get:45 http://172.17.0.1/private bullseye-staging/main armhf libcurl4 armhf 7.74.0-1.2 [305 kB]
Get:46 http://172.17.0.1/private bullseye-staging/main armhf libjsoncpp24 armhf 1.9.4-4 [67.0 kB]
Get:47 http://172.17.0.1/private bullseye-staging/main armhf librhash0 armhf 1.4.1-1 [140 kB]
Get:48 http://172.17.0.1/private bullseye-staging/main armhf libuv1 armhf 1.40.0-1 [118 kB]
Get:49 http://172.17.0.1/private bullseye-staging/main armhf cmake armhf 3.18.4-2+rpi1 [3118 kB]
Get:50 http://172.17.0.1/private bullseye-staging/main armhf libdebhelper-perl all 13.3.4 [189 kB]
Get:51 http://172.17.0.1/private bullseye-staging/main armhf libtool all 2.4.6-15 [513 kB]
Get:52 http://172.17.0.1/private bullseye-staging/main armhf dh-autoreconf all 20 [17.1 kB]
Get:53 http://172.17.0.1/private bullseye-staging/main armhf libarchive-zip-perl all 1.68-1 [104 kB]
Get:54 http://172.17.0.1/private bullseye-staging/main armhf libsub-override-perl all 0.09-2 [10.2 kB]
Get:55 http://172.17.0.1/private bullseye-staging/main armhf libfile-stripnondeterminism-perl all 1.11.0-1 [25.6 kB]
Get:56 http://172.17.0.1/private bullseye-staging/main armhf dh-strip-nondeterminism all 1.11.0-1 [15.3 kB]
Get:57 http://172.17.0.1/private bullseye-staging/main armhf libelf1 armhf 0.183-1 [161 kB]
Get:58 http://172.17.0.1/private bullseye-staging/main armhf dwz armhf 0.13+20210201-1 [164 kB]
Get:59 http://172.17.0.1/private bullseye-staging/main armhf gettext armhf 0.21-4 [1215 kB]
Get:60 http://172.17.0.1/private bullseye-staging/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB]
Get:61 http://172.17.0.1/private bullseye-staging/main armhf po-debconf all 1.0.21+nmu1 [248 kB]
Get:62 http://172.17.0.1/private bullseye-staging/main armhf debhelper all 13.3.4 [1049 kB]
Get:63 http://172.17.0.1/private bullseye-staging/main armhf distro-info-data all 0.46 [7192 B]
Get:64 http://172.17.0.1/private bullseye-staging/main armhf libgfortran5 armhf 10.2.1-6+rpi1 [232 kB]
Get:65 http://172.17.0.1/private bullseye-staging/main armhf libgfortran-10-dev armhf 10.2.1-6+rpi1 [278 kB]
Get:66 http://172.17.0.1/private bullseye-staging/main armhf gfortran-10 armhf 10.2.1-6+rpi1 [7195 kB]
Get:67 http://172.17.0.1/private bullseye-staging/main armhf gfortran armhf 4:10.2.1-1+rpi1 [1428 B]
Get:68 http://172.17.0.1/private bullseye-staging/main armhf libhwloc15 armhf 2.4.1+dfsg-1 [122 kB]
Get:69 http://172.17.0.1/private bullseye-staging/main armhf hwloc-nox armhf 2.4.1+dfsg-1 [167 kB]
Get:70 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-200 armhf 3.4.0-1 [55.0 kB]
Get:71 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-200 armhf 3.4.0-1 [132 kB]
Get:72 http://172.17.0.1/private bullseye-staging/main armhf libibverbs1 armhf 33.1-1 [51.7 kB]
Get:73 http://172.17.0.1/private bullseye-staging/main armhf ibverbs-providers armhf 33.1-1 [24.4 kB]
Get:74 http://172.17.0.1/private bullseye-staging/main armhf libblas3 armhf 3.9.0-3 [108 kB]
Get:75 http://172.17.0.1/private bullseye-staging/main armhf libblas-dev armhf 3.9.0-3 [113 kB]
Get:76 http://172.17.0.1/private bullseye-staging/main armhf libboost1.74-dev armhf 1.74.0-9 [9534 kB]
Get:77 http://172.17.0.1/private bullseye-staging/main armhf libboost-dev armhf 1.74.0.3+b1 [4820 B]
Get:78 http://172.17.0.1/private bullseye-staging/main armhf libevent-2.1-7 armhf 2.1.12-stable-1 [167 kB]
Get:79 http://172.17.0.1/private bullseye-staging/main armhf libevent-core-2.1-7 armhf 2.1.12-stable-1 [126 kB]
Get:80 http://172.17.0.1/private bullseye-staging/main armhf libevent-extra-2.1-7 armhf 2.1.12-stable-1 [100 kB]
Get:81 http://172.17.0.1/private bullseye-staging/main armhf libevent-pthreads-2.1-7 armhf 2.1.12-stable-1 [56.8 kB]
Get:82 http://172.17.0.1/private bullseye-staging/main armhf libevent-openssl-2.1-7 armhf 2.1.12-stable-1 [61.7 kB]
Get:83 http://172.17.0.1/private bullseye-staging/main armhf libevent-dev armhf 2.1.12-stable-1 [281 kB]
Get:84 http://172.17.0.1/private bullseye-staging/main armhf librdmacm1 armhf 33.1-1 [59.3 kB]
Get:85 http://172.17.0.1/private bullseye-staging/main armhf libfabric1 armhf 1.11.0-2 [311 kB]
Get:86 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-double3 armhf 3.3.8-2 [429 kB]
Get:87 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-single3 armhf 3.3.8-2 [633 kB]
Get:88 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-bin armhf 3.3.8-2 [43.6 kB]
Get:89 http://172.17.0.1/private bullseye-staging/main armhf libfftw3-dev armhf 3.3.8-2 [1060 kB]
Get:90 http://172.17.0.1/private bullseye-staging/main armhf libnuma1 armhf 2.0.12-1 [22.5 kB]
Get:91 http://172.17.0.1/private bullseye-staging/main armhf libnuma-dev armhf 2.0.12-1 [35.6 kB]
Get:92 http://172.17.0.1/private bullseye-staging/main armhf libltdl7 armhf 2.4.6-15 [388 kB]
Get:93 http://172.17.0.1/private bullseye-staging/main armhf libltdl-dev armhf 2.4.6-15 [159 kB]
Get:94 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-dev armhf 2.4.1+dfsg-1 [190 kB]
Get:95 http://172.17.0.1/private bullseye-staging/main armhf libpciaccess0 armhf 0.16-1 [51.0 kB]
Get:96 http://172.17.0.1/private bullseye-staging/main armhf libxau6 armhf 1:1.0.9-1 [19.1 kB]
Get:97 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp6 armhf 1:1.1.2-3 [25.0 kB]
Get:98 http://172.17.0.1/private bullseye-staging/main armhf libxcb1 armhf 1.14-3 [136 kB]
Get:99 http://172.17.0.1/private bullseye-staging/main armhf libx11-data all 2:1.7.0-2 [310 kB]
Get:100 http://172.17.0.1/private bullseye-staging/main armhf libx11-6 armhf 2:1.7.0-2 [706 kB]
Get:101 http://172.17.0.1/private bullseye-staging/main armhf libxext6 armhf 2:1.3.3-1.1 [47.8 kB]
Get:102 http://172.17.0.1/private bullseye-staging/main armhf libxnvctrl0 armhf 460.56-1 [25.7 kB]
Get:103 http://172.17.0.1/private bullseye-staging/main armhf ocl-icd-libopencl1 armhf 2.2.14-2 [39.9 kB]
Get:104 http://172.17.0.1/private bullseye-staging/main armhf libhwloc-plugins armhf 2.4.1+dfsg-1 [19.9 kB]
Get:105 http://172.17.0.1/private bullseye-staging/main armhf libnl-3-dev armhf 3.4.0-1 [92.4 kB]
Get:106 http://172.17.0.1/private bullseye-staging/main armhf libnl-route-3-dev armhf 3.4.0-1 [145 kB]
Get:107 http://172.17.0.1/private bullseye-staging/main armhf libibverbs-dev armhf 33.1-1 [178 kB]
Get:108 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery all 3.5.1+dfsg+~3.5.5-7 [315 kB]
Get:109 http://172.17.0.1/private bullseye-staging/main armhf libjs-jquery-ui all 1.12.1+dfsg-8 [232 kB]
Get:110 http://172.17.0.1/private bullseye-staging/main armhf liblapack3 armhf 3.9.0-3 [1597 kB]
Get:111 http://172.17.0.1/private bullseye-staging/main armhf liblapack-dev armhf 3.9.0-3 [2980 kB]
Get:112 http://172.17.0.1/private bullseye-staging/main armhf libmpich12 armhf 3.4.1-3 [1530 kB]
Get:113 http://172.17.0.1/private bullseye-staging/main armhf libslurm36 armhf 20.11.4-1 [586 kB]
Get:114 http://172.17.0.1/private bullseye-staging/main armhf mpich armhf 3.4.1-3 [188 kB]
Get:115 http://172.17.0.1/private bullseye-staging/main armhf libmpich-dev armhf 3.4.1-3 [1893 kB]
Get:116 http://172.17.0.1/private bullseye-staging/main armhf libpmix2 armhf 4.0.0-4 [466 kB]
Get:117 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi3 armhf 4.1.0-8+rpi1 [1768 kB]
Get:118 http://172.17.0.1/private bullseye-staging/main armhf openmpi-common all 4.1.0-8+rpi1 [177 kB]
Get:119 http://172.17.0.1/private bullseye-staging/main armhf libpmix-dev armhf 4.0.0-4 [602 kB]
Get:120 http://172.17.0.1/private bullseye-staging/main armhf zlib1g-dev armhf 1:1.2.11.dfsg-2 [184 kB]
Get:121 http://172.17.0.1/private bullseye-staging/main armhf openmpi-bin armhf 4.1.0-8+rpi1 [205 kB]
Get:122 http://172.17.0.1/private bullseye-staging/main armhf libopenmpi-dev armhf 4.1.0-8+rpi1 [1143 kB]
Get:123 http://172.17.0.1/private bullseye-staging/main armhf libpthread-stubs0-dev armhf 0.4-1 [5344 B]
Get:124 http://172.17.0.1/private bullseye-staging/main armhf xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB]
Get:125 http://172.17.0.1/private bullseye-staging/main armhf x11proto-dev all 2020.1-1 [594 kB]
Get:126 http://172.17.0.1/private bullseye-staging/main armhf libxau-dev armhf 1:1.0.9-1 [22.3 kB]
Get:127 http://172.17.0.1/private bullseye-staging/main armhf libxdmcp-dev armhf 1:1.1.2-3 [40.9 kB]
Get:128 http://172.17.0.1/private bullseye-staging/main armhf xtrans-dev all 1.4.0-1 [98.7 kB]
Get:129 http://172.17.0.1/private bullseye-staging/main armhf libxcb1-dev armhf 1.14-3 [171 kB]
Get:130 http://172.17.0.1/private bullseye-staging/main armhf libx11-dev armhf 2:1.7.0-2 [777 kB]
Get:131 http://172.17.0.1/private bullseye-staging/main armhf lsb-release all 11.1.0+rpi1 [28.1 kB]
debconf: delaying package configuration, since apt-utils is not installed
Fetched 69.8 MB in 25s (2787 kB/s)
Selecting previously unselected package libuchardet0:armhf.
(Reading database ... 12579 files and directories currently installed.)
Preparing to unpack .../0-libuchardet0_0.0.7-1_armhf.deb ...
Unpacking libuchardet0:armhf (0.0.7-1) ...
Selecting previously unselected package groff-base.
Preparing to unpack .../1-groff-base_1.22.4-6_armhf.deb ...
Unpacking groff-base (1.22.4-6) ...
Selecting previously unselected package libpipeline1:armhf.
Preparing to unpack .../2-libpipeline1_1.5.3-1_armhf.deb ...
Unpacking libpipeline1:armhf (1.5.3-1) ...
Selecting previously unselected package man-db.
Preparing to unpack .../3-man-db_2.9.4-2_armhf.deb ...
Unpacking man-db (2.9.4-2) ...
Selecting previously unselected package libpython3.9-minimal:armhf.
Preparing to unpack .../4-libpython3.9-minimal_3.9.2-1+rpi1_armhf.deb ...
Unpacking libpython3.9-minimal:armhf (3.9.2-1+rpi1) ...
Selecting previously unselected package libexpat1:armhf.
Preparing to unpack .../5-libexpat1_2.2.10-2_armhf.deb ...
Unpacking libexpat1:armhf (2.2.10-2) ...
Selecting previously unselected package python3.9-minimal.
Preparing to unpack .../6-python3.9-minimal_3.9.2-1+rpi1_armhf.deb ...
Unpacking python3.9-minimal (3.9.2-1+rpi1) ...
Setting up libpython3.9-minimal:armhf (3.9.2-1+rpi1) ...
Setting up libexpat1:armhf (2.2.10-2) ...
Setting up python3.9-minimal (3.9.2-1+rpi1) ...
Selecting previously unselected package python3-minimal.
(Reading database ... 13415 files and directories currently installed.)
Preparing to unpack .../0-python3-minimal_3.9.2-2_armhf.deb ...
Unpacking python3-minimal (3.9.2-2) ...
Selecting previously unselected package media-types.
Preparing to unpack .../1-media-types_4.0.0_all.deb ...
Unpacking media-types (4.0.0) ...
Selecting previously unselected package libmpdec3:armhf.
Preparing to unpack .../2-libmpdec3_2.5.1-1+rpi1_armhf.deb ...
Unpacking libmpdec3:armhf (2.5.1-1+rpi1) ...
Selecting previously unselected package libpython3.9-stdlib:armhf.
Preparing to unpack .../3-libpython3.9-stdlib_3.9.2-1+rpi1_armhf.deb ...
Unpacking libpython3.9-stdlib:armhf (3.9.2-1+rpi1) ...
Selecting previously unselected package python3.9.
Preparing to unpack .../4-python3.9_3.9.2-1+rpi1_armhf.deb ...
Unpacking python3.9 (3.9.2-1+rpi1) ...
Selecting previously unselected package libpython3-stdlib:armhf.
Preparing to unpack .../5-libpython3-stdlib_3.9.2-2_armhf.deb ...
Unpacking libpython3-stdlib:armhf (3.9.2-2) ...
Setting up python3-minimal (3.9.2-2) ...
Selecting previously unselected package python3.
(Reading database ... 13812 files and directories currently installed.)
Preparing to unpack .../000-python3_3.9.2-2_armhf.deb ...
Unpacking python3 (3.9.2-2) ...
Selecting previously unselected package libncurses6:armhf.
Preparing to unpack .../001-libncurses6_6.2+20201114-2_armhf.deb ...
Unpacking libncurses6:armhf (6.2+20201114-2) ...
Selecting previously unselected package libprocps8:armhf.
Preparing to unpack .../002-libprocps8_2%3a3.3.17-5_armhf.deb ...
Unpacking libprocps8:armhf (2:3.3.17-5) ...
Selecting previously unselected package procps.
Preparing to unpack .../003-procps_2%3a3.3.17-5_armhf.deb ...
Unpacking procps (2:3.3.17-5) ...
Selecting previously unselected package libmagic-mgc.
Preparing to unpack .../004-libmagic-mgc_1%3a5.39-3_armhf.deb ...
Unpacking libmagic-mgc (1:5.39-3) ...
Selecting previously unselected package libmagic1:armhf.
Preparing to unpack .../005-libmagic1_1%3a5.39-3_armhf.deb ...
Unpacking libmagic1:armhf (1:5.39-3) ...
Selecting previously unselected package file.
Preparing to unpack .../006-file_1%3a5.39-3_armhf.deb ...
Unpacking file (1:5.39-3) ...
Selecting previously unselected package gettext-base.
Preparing to unpack .../007-gettext-base_0.21-4_armhf.deb ...
Unpacking gettext-base (0.21-4) ...
Selecting previously unselected package libmd0:armhf.
Preparing to unpack .../008-libmd0_1.0.3-3_armhf.deb ...
Unpacking libmd0:armhf (1.0.3-3) ...
Selecting previously unselected package libbsd0:armhf.
Preparing to unpack .../009-libbsd0_0.11.3-1_armhf.deb ...
Unpacking libbsd0:armhf (0.11.3-1) ...
Selecting previously unselected package libedit2:armhf.
Preparing to unpack .../010-libedit2_3.1-20191231-2_armhf.deb ...
Unpacking libedit2:armhf (3.1-20191231-2) ...
Selecting previously unselected package libcbor0:armhf.
Preparing to unpack .../011-libcbor0_0.5.0+dfsg-2_armhf.deb ...
Unpacking libcbor0:armhf (0.5.0+dfsg-2) ...
Selecting previously unselected package libfido2-1:armhf.
Preparing to unpack .../012-libfido2-1_1.6.0-2_armhf.deb ...
Unpacking libfido2-1:armhf (1.6.0-2) ...
Selecting previously unselected package openssh-client.
Preparing to unpack .../013-openssh-client_1%3a8.4p1-5_armhf.deb ...
Unpacking openssh-client (1:8.4p1-5) ...
Selecting previously unselected package libsigsegv2:armhf.
Preparing to unpack .../014-libsigsegv2_2.13-1_armhf.deb ...
Unpacking libsigsegv2:armhf (2.13-1) ...
Selecting previously unselected package m4.
Preparing to unpack .../015-m4_1.4.18-5_armhf.deb ...
Unpacking m4 (1.4.18-5) ...
Selecting previously unselected package autoconf.
Preparing to unpack .../016-autoconf_2.69-14_all.deb ...
Unpacking autoconf (2.69-14) ...
Selecting previously unselected package autotools-dev.
Preparing to unpack .../017-autotools-dev_20180224.1+nmu1_all.deb ...
Unpacking autotools-dev (20180224.1+nmu1) ...
Selecting previously unselected package automake.
Preparing to unpack .../018-automake_1%3a1.16.3-2_all.deb ...
Unpacking automake (1:1.16.3-2) ...
Selecting previously unselected package autopoint.
Preparing to unpack .../019-autopoint_0.21-4_all.deb ...
Unpacking autopoint (0.21-4) ...
Selecting previously unselected package chrpath.
Preparing to unpack .../020-chrpath_0.16-2_armhf.deb ...
Unpacking chrpath (0.16-2) ...
Selecting previously unselected package cmake-data.
Preparing to unpack .../021-cmake-data_3.18.4-2+rpi1_all.deb ...
Unpacking cmake-data (3.18.4-2+rpi1) ...
Selecting previously unselected package libicu67:armhf.
Preparing to unpack .../022-libicu67_67.1-6_armhf.deb ...
Unpacking libicu67:armhf (67.1-6) ...
Selecting previously unselected package libxml2:armhf.
Preparing to unpack .../023-libxml2_2.9.10+dfsg-6.3_armhf.deb ...
Unpacking libxml2:armhf (2.9.10+dfsg-6.3) ...
Selecting previously unselected package libarchive13:armhf.
Preparing to unpack .../024-libarchive13_3.4.3-2_armhf.deb ...
Unpacking libarchive13:armhf (3.4.3-2) ...
Selecting previously unselected package libbrotli1:armhf.
Preparing to unpack .../025-libbrotli1_1.0.9-2+b1_armhf.deb ...
Unpacking libbrotli1:armhf (1.0.9-2+b1) ...
Selecting previously unselected package libnghttp2-14:armhf.
Preparing to unpack .../026-libnghttp2-14_1.43.0-1_armhf.deb ...
Unpacking libnghttp2-14:armhf (1.43.0-1) ...
Selecting previously unselected package libpsl5:armhf.
Preparing to unpack .../027-libpsl5_0.21.0-1.2_armhf.deb ...
Unpacking libpsl5:armhf (0.21.0-1.2) ...
Selecting previously unselected package librtmp1:armhf.
Preparing to unpack .../028-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_armhf.deb ...
Unpacking librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Selecting previously unselected package libssh2-1:armhf.
Preparing to unpack .../029-libssh2-1_1.9.0-2_armhf.deb ...
Unpacking libssh2-1:armhf (1.9.0-2) ...
Selecting previously unselected package libcurl4:armhf.
Preparing to unpack .../030-libcurl4_7.74.0-1.2_armhf.deb ...
Unpacking libcurl4:armhf (7.74.0-1.2) ...
Selecting previously unselected package libjsoncpp24:armhf.
Preparing to unpack .../031-libjsoncpp24_1.9.4-4_armhf.deb ...
Unpacking libjsoncpp24:armhf (1.9.4-4) ...
Selecting previously unselected package librhash0:armhf.
Preparing to unpack .../032-librhash0_1.4.1-1_armhf.deb ...
Unpacking librhash0:armhf (1.4.1-1) ...
Selecting previously unselected package libuv1:armhf.
Preparing to unpack .../033-libuv1_1.40.0-1_armhf.deb ...
Unpacking libuv1:armhf (1.40.0-1) ...
Selecting previously unselected package cmake.
Preparing to unpack .../034-cmake_3.18.4-2+rpi1_armhf.deb ...
Unpacking cmake (3.18.4-2+rpi1) ...
Selecting previously unselected package libdebhelper-perl.
Preparing to unpack .../035-libdebhelper-perl_13.3.4_all.deb ...
Unpacking libdebhelper-perl (13.3.4) ...
Selecting previously unselected package libtool.
Preparing to unpack .../036-libtool_2.4.6-15_all.deb ...
Unpacking libtool (2.4.6-15) ...
Selecting previously unselected package dh-autoreconf.
Preparing to unpack .../037-dh-autoreconf_20_all.deb ...
Unpacking dh-autoreconf (20) ...
Selecting previously unselected package libarchive-zip-perl.
Preparing to unpack .../038-libarchive-zip-perl_1.68-1_all.deb ...
Unpacking libarchive-zip-perl (1.68-1) ...
Selecting previously unselected package libsub-override-perl.
Preparing to unpack .../039-libsub-override-perl_0.09-2_all.deb ...
Unpacking libsub-override-perl (0.09-2) ...
Selecting previously unselected package libfile-stripnondeterminism-perl.
Preparing to unpack .../040-libfile-stripnondeterminism-perl_1.11.0-1_all.deb ...
Unpacking libfile-stripnondeterminism-perl (1.11.0-1) ...
Selecting previously unselected package dh-strip-nondeterminism.
Preparing to unpack .../041-dh-strip-nondeterminism_1.11.0-1_all.deb ...
Unpacking dh-strip-nondeterminism (1.11.0-1) ...
Selecting previously unselected package libelf1:armhf.
Preparing to unpack .../042-libelf1_0.183-1_armhf.deb ...
Unpacking libelf1:armhf (0.183-1) ...
Selecting previously unselected package dwz.
Preparing to unpack .../043-dwz_0.13+20210201-1_armhf.deb ...
Unpacking dwz (0.13+20210201-1) ...
Selecting previously unselected package gettext.
Preparing to unpack .../044-gettext_0.21-4_armhf.deb ...
Unpacking gettext (0.21-4) ...
Selecting previously unselected package intltool-debian.
Preparing to unpack .../045-intltool-debian_0.35.0+20060710.5_all.deb ...
Unpacking intltool-debian (0.35.0+20060710.5) ...
Selecting previously unselected package po-debconf.
Preparing to unpack .../046-po-debconf_1.0.21+nmu1_all.deb ...
Unpacking po-debconf (1.0.21+nmu1) ...
Selecting previously unselected package debhelper.
Preparing to unpack .../047-debhelper_13.3.4_all.deb ...
Unpacking debhelper (13.3.4) ...
Selecting previously unselected package distro-info-data.
Preparing to unpack .../048-distro-info-data_0.46_all.deb ...
Unpacking distro-info-data (0.46) ...
Selecting previously unselected package libgfortran5:armhf.
Preparing to unpack .../049-libgfortran5_10.2.1-6+rpi1_armhf.deb ...
Unpacking libgfortran5:armhf (10.2.1-6+rpi1) ...
Selecting previously unselected package libgfortran-10-dev:armhf.
Preparing to unpack .../050-libgfortran-10-dev_10.2.1-6+rpi1_armhf.deb ...
Unpacking libgfortran-10-dev:armhf (10.2.1-6+rpi1) ...
Selecting previously unselected package gfortran-10.
Preparing to unpack .../051-gfortran-10_10.2.1-6+rpi1_armhf.deb ...
Unpacking gfortran-10 (10.2.1-6+rpi1) ...
Selecting previously unselected package gfortran.
Preparing to unpack .../052-gfortran_4%3a10.2.1-1+rpi1_armhf.deb ...
Unpacking gfortran (4:10.2.1-1+rpi1) ...
Selecting previously unselected package libhwloc15:armhf.
Preparing to unpack .../053-libhwloc15_2.4.1+dfsg-1_armhf.deb ...
Unpacking libhwloc15:armhf (2.4.1+dfsg-1) ...
Selecting previously unselected package hwloc-nox.
Preparing to unpack .../054-hwloc-nox_2.4.1+dfsg-1_armhf.deb ...
Unpacking hwloc-nox (2.4.1+dfsg-1) ...
Selecting previously unselected package libnl-3-200:armhf.
Preparing to unpack .../055-libnl-3-200_3.4.0-1_armhf.deb ...
Unpacking libnl-3-200:armhf (3.4.0-1) ...
Selecting previously unselected package libnl-route-3-200:armhf.
Preparing to unpack .../056-libnl-route-3-200_3.4.0-1_armhf.deb ...
Unpacking libnl-route-3-200:armhf (3.4.0-1) ...
Selecting previously unselected package libibverbs1:armhf.
Preparing to unpack .../057-libibverbs1_33.1-1_armhf.deb ...
Unpacking libibverbs1:armhf (33.1-1) ...
Selecting previously unselected package ibverbs-providers:armhf.
Preparing to unpack .../058-ibverbs-providers_33.1-1_armhf.deb ...
Unpacking ibverbs-providers:armhf (33.1-1) ...
Selecting previously unselected package libblas3:armhf.
Preparing to unpack .../059-libblas3_3.9.0-3_armhf.deb ...
Unpacking libblas3:armhf (3.9.0-3) ...
Selecting previously unselected package libblas-dev:armhf.
Preparing to unpack .../060-libblas-dev_3.9.0-3_armhf.deb ...
Unpacking libblas-dev:armhf (3.9.0-3) ...
Selecting previously unselected package libboost1.74-dev:armhf.
Preparing to unpack .../061-libboost1.74-dev_1.74.0-9_armhf.deb ...
Unpacking libboost1.74-dev:armhf (1.74.0-9) ...
Selecting previously unselected package libboost-dev:armhf.
Preparing to unpack .../062-libboost-dev_1.74.0.3+b1_armhf.deb ...
Unpacking libboost-dev:armhf (1.74.0.3+b1) ...
Selecting previously unselected package libevent-2.1-7:armhf.
Preparing to unpack .../063-libevent-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-core-2.1-7:armhf.
Preparing to unpack .../064-libevent-core-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-core-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-extra-2.1-7:armhf.
Preparing to unpack .../065-libevent-extra-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-extra-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-pthreads-2.1-7:armhf.
Preparing to unpack .../066-libevent-pthreads-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-openssl-2.1-7:armhf.
Preparing to unpack .../067-libevent-openssl-2.1-7_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
Selecting previously unselected package libevent-dev.
Preparing to unpack .../068-libevent-dev_2.1.12-stable-1_armhf.deb ...
Unpacking libevent-dev (2.1.12-stable-1) ...
Selecting previously unselected package librdmacm1:armhf.
Preparing to unpack .../069-librdmacm1_33.1-1_armhf.deb ...
Unpacking librdmacm1:armhf (33.1-1) ...
Selecting previously unselected package libfabric1.
Preparing to unpack .../070-libfabric1_1.11.0-2_armhf.deb ...
Unpacking libfabric1 (1.11.0-2) ...
Selecting previously unselected package libfftw3-double3:armhf.
Preparing to unpack .../071-libfftw3-double3_3.3.8-2_armhf.deb ...
Unpacking libfftw3-double3:armhf (3.3.8-2) ...
Selecting previously unselected package libfftw3-single3:armhf.
Preparing to unpack .../072-libfftw3-single3_3.3.8-2_armhf.deb ...
Unpacking libfftw3-single3:armhf (3.3.8-2) ...
Selecting previously unselected package libfftw3-bin.
Preparing to unpack .../073-libfftw3-bin_3.3.8-2_armhf.deb ...
Unpacking libfftw3-bin (3.3.8-2) ...
Selecting previously unselected package libfftw3-dev:armhf.
Preparing to unpack .../074-libfftw3-dev_3.3.8-2_armhf.deb ...
Unpacking libfftw3-dev:armhf (3.3.8-2) ...
Selecting previously unselected package libnuma1:armhf.
Preparing to unpack .../075-libnuma1_2.0.12-1_armhf.deb ...
Unpacking libnuma1:armhf (2.0.12-1) ...
Selecting previously unselected package libnuma-dev:armhf.
Preparing to unpack .../076-libnuma-dev_2.0.12-1_armhf.deb ...
Unpacking libnuma-dev:armhf (2.0.12-1) ...
Selecting previously unselected package libltdl7:armhf.
Preparing to unpack .../077-libltdl7_2.4.6-15_armhf.deb ...
Unpacking libltdl7:armhf (2.4.6-15) ...
Selecting previously unselected package libltdl-dev:armhf.
Preparing to unpack .../078-libltdl-dev_2.4.6-15_armhf.deb ...
Unpacking libltdl-dev:armhf (2.4.6-15) ...
Selecting previously unselected package libhwloc-dev:armhf.
Preparing to unpack .../079-libhwloc-dev_2.4.1+dfsg-1_armhf.deb ...
Unpacking libhwloc-dev:armhf (2.4.1+dfsg-1) ...
Selecting previously unselected package libpciaccess0:armhf.
Preparing to unpack .../080-libpciaccess0_0.16-1_armhf.deb ...
Unpacking libpciaccess0:armhf (0.16-1) ...
Selecting previously unselected package libxau6:armhf.
Preparing to unpack .../081-libxau6_1%3a1.0.9-1_armhf.deb ...
Unpacking libxau6:armhf (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp6:armhf.
Preparing to unpack .../082-libxdmcp6_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp6:armhf (1:1.1.2-3) ...
Selecting previously unselected package libxcb1:armhf.
Preparing to unpack .../083-libxcb1_1.14-3_armhf.deb ...
Unpacking libxcb1:armhf (1.14-3) ...
Selecting previously unselected package libx11-data.
Preparing to unpack .../084-libx11-data_2%3a1.7.0-2_all.deb ...
Unpacking libx11-data (2:1.7.0-2) ...
Selecting previously unselected package libx11-6:armhf.
Preparing to unpack .../085-libx11-6_2%3a1.7.0-2_armhf.deb ...
Unpacking libx11-6:armhf (2:1.7.0-2) ...
Selecting previously unselected package libxext6:armhf.
Preparing to unpack .../086-libxext6_2%3a1.3.3-1.1_armhf.deb ...
Unpacking libxext6:armhf (2:1.3.3-1.1) ...
Selecting previously unselected package libxnvctrl0:armhf.
Preparing to unpack .../087-libxnvctrl0_460.56-1_armhf.deb ...
Unpacking libxnvctrl0:armhf (460.56-1) ...
Selecting previously unselected package ocl-icd-libopencl1:armhf.
Preparing to unpack .../088-ocl-icd-libopencl1_2.2.14-2_armhf.deb ...
Unpacking ocl-icd-libopencl1:armhf (2.2.14-2) ...
Selecting previously unselected package libhwloc-plugins:armhf.
Preparing to unpack .../089-libhwloc-plugins_2.4.1+dfsg-1_armhf.deb ...
Unpacking libhwloc-plugins:armhf (2.4.1+dfsg-1) ...
Selecting previously unselected package libnl-3-dev:armhf.
Preparing to unpack .../090-libnl-3-dev_3.4.0-1_armhf.deb ...
Unpacking libnl-3-dev:armhf (3.4.0-1) ...
Selecting previously unselected package libnl-route-3-dev:armhf.
Preparing to unpack .../091-libnl-route-3-dev_3.4.0-1_armhf.deb ...
Unpacking libnl-route-3-dev:armhf (3.4.0-1) ...
Selecting previously unselected package libibverbs-dev:armhf.
Preparing to unpack .../092-libibverbs-dev_33.1-1_armhf.deb ...
Unpacking libibverbs-dev:armhf (33.1-1) ...
Selecting previously unselected package libjs-jquery.
Preparing to unpack .../093-libjs-jquery_3.5.1+dfsg+~3.5.5-7_all.deb ...
Unpacking libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Selecting previously unselected package libjs-jquery-ui.
Preparing to unpack .../094-libjs-jquery-ui_1.12.1+dfsg-8_all.deb ...
Unpacking libjs-jquery-ui (1.12.1+dfsg-8) ...
Selecting previously unselected package liblapack3:armhf.
Preparing to unpack .../095-liblapack3_3.9.0-3_armhf.deb ...
Unpacking liblapack3:armhf (3.9.0-3) ...
Selecting previously unselected package liblapack-dev:armhf.
Preparing to unpack .../096-liblapack-dev_3.9.0-3_armhf.deb ...
Unpacking liblapack-dev:armhf (3.9.0-3) ...
Selecting previously unselected package libmpich12:armhf.
Preparing to unpack .../097-libmpich12_3.4.1-3_armhf.deb ...
Unpacking libmpich12:armhf (3.4.1-3) ...
Selecting previously unselected package libslurm36.
Preparing to unpack .../098-libslurm36_20.11.4-1_armhf.deb ...
Unpacking libslurm36 (20.11.4-1) ...
Selecting previously unselected package mpich.
Preparing to unpack .../099-mpich_3.4.1-3_armhf.deb ...
Unpacking mpich (3.4.1-3) ...
Selecting previously unselected package libmpich-dev:armhf.
Preparing to unpack .../100-libmpich-dev_3.4.1-3_armhf.deb ...
Unpacking libmpich-dev:armhf (3.4.1-3) ...
Selecting previously unselected package libpmix2:armhf.
Preparing to unpack .../101-libpmix2_4.0.0-4_armhf.deb ...
Unpacking libpmix2:armhf (4.0.0-4) ...
Selecting previously unselected package libopenmpi3:armhf.
Preparing to unpack .../102-libopenmpi3_4.1.0-8+rpi1_armhf.deb ...
Unpacking libopenmpi3:armhf (4.1.0-8+rpi1) ...
Selecting previously unselected package openmpi-common.
Preparing to unpack .../103-openmpi-common_4.1.0-8+rpi1_all.deb ...
Unpacking openmpi-common (4.1.0-8+rpi1) ...
Selecting previously unselected package libpmix-dev:armhf.
Preparing to unpack .../104-libpmix-dev_4.0.0-4_armhf.deb ...
Unpacking libpmix-dev:armhf (4.0.0-4) ...
Selecting previously unselected package zlib1g-dev:armhf.
Preparing to unpack .../105-zlib1g-dev_1%3a1.2.11.dfsg-2_armhf.deb ...
Unpacking zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Selecting previously unselected package openmpi-bin.
Preparing to unpack .../106-openmpi-bin_4.1.0-8+rpi1_armhf.deb ...
Unpacking openmpi-bin (4.1.0-8+rpi1) ...
Selecting previously unselected package libopenmpi-dev:armhf.
Preparing to unpack .../107-libopenmpi-dev_4.1.0-8+rpi1_armhf.deb ...
Unpacking libopenmpi-dev:armhf (4.1.0-8+rpi1) ...
Selecting previously unselected package libpthread-stubs0-dev:armhf.
Preparing to unpack .../108-libpthread-stubs0-dev_0.4-1_armhf.deb ...
Unpacking libpthread-stubs0-dev:armhf (0.4-1) ...
Selecting previously unselected package xorg-sgml-doctools.
Preparing to unpack .../109-xorg-sgml-doctools_1%3a1.11-1.1_all.deb ...
Unpacking xorg-sgml-doctools (1:1.11-1.1) ...
Selecting previously unselected package x11proto-dev.
Preparing to unpack .../110-x11proto-dev_2020.1-1_all.deb ...
Unpacking x11proto-dev (2020.1-1) ...
Selecting previously unselected package libxau-dev:armhf.
Preparing to unpack .../111-libxau-dev_1%3a1.0.9-1_armhf.deb ...
Unpacking libxau-dev:armhf (1:1.0.9-1) ...
Selecting previously unselected package libxdmcp-dev:armhf.
Preparing to unpack .../112-libxdmcp-dev_1%3a1.1.2-3_armhf.deb ...
Unpacking libxdmcp-dev:armhf (1:1.1.2-3) ...
Selecting previously unselected package xtrans-dev.
Preparing to unpack .../113-xtrans-dev_1.4.0-1_all.deb ...
Unpacking xtrans-dev (1.4.0-1) ...
Selecting previously unselected package libxcb1-dev:armhf.
Preparing to unpack .../114-libxcb1-dev_1.14-3_armhf.deb ...
Unpacking libxcb1-dev:armhf (1.14-3) ...
Selecting previously unselected package libx11-dev:armhf.
Preparing to unpack .../115-libx11-dev_2%3a1.7.0-2_armhf.deb ...
Unpacking libx11-dev:armhf (2:1.7.0-2) ...
Selecting previously unselected package lsb-release.
Preparing to unpack .../116-lsb-release_11.1.0+rpi1_all.deb ...
Unpacking lsb-release (11.1.0+rpi1) ...
Selecting previously unselected package sbuild-build-depends-gromacs-dummy.
Preparing to unpack .../117-sbuild-build-depends-gromacs-dummy_0.invalid.0_armhf.deb ...
Unpacking sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Setting up media-types (4.0.0) ...
Setting up libslurm36 (20.11.4-1) ...
Setting up libpipeline1:armhf (1.5.3-1) ...
Setting up libpciaccess0:armhf (0.16-1) ...
Setting up libxau6:armhf (1:1.0.9-1) ...
Setting up libpsl5:armhf (0.21.0-1.2) ...
Setting up libboost1.74-dev:armhf (1.74.0-9) ...
Setting up libfftw3-single3:armhf (3.3.8-2) ...
Setting up libicu67:armhf (67.1-6) ...
Setting up libmagic-mgc (1:5.39-3) ...
Setting up libarchive-zip-perl (1.68-1) ...
Setting up distro-info-data (0.46) ...
Setting up libdebhelper-perl (13.3.4) ...
Setting up libbrotli1:armhf (1.0.9-2+b1) ...
Setting up libcbor0:armhf (0.5.0+dfsg-2) ...
Setting up libnghttp2-14:armhf (1.43.0-1) ...
Setting up libmagic1:armhf (1:5.39-3) ...
Setting up gettext-base (0.21-4) ...
Setting up file (1:5.39-3) ...
Setting up libpthread-stubs0-dev:armhf (0.4-1) ...
Setting up xtrans-dev (1.4.0-1) ...
Setting up autotools-dev (20180224.1+nmu1) ...
Setting up libblas3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode
Setting up libuv1:armhf (1.40.0-1) ...
Setting up libx11-data (2:1.7.0-2) ...
Setting up librtmp1:armhf (2.4+20151223.gitfa8646d.1-2+b2) ...
Setting up libncurses6:armhf (6.2+20201114-2) ...
Setting up libsigsegv2:armhf (2.13-1) ...
Setting up libhwloc15:armhf (2.4.1+dfsg-1) ...
Setting up libevent-core-2.1-7:armhf (2.1.12-stable-1) ...
Setting up libevent-2.1-7:armhf (2.1.12-stable-1) ...
Setting up autopoint (0.21-4) ...
Setting up libltdl7:armhf (2.4.6-15) ...
Setting up libfftw3-double3:armhf (3.3.8-2) ...
Setting up libgfortran5:armhf (10.2.1-6+rpi1) ...
Setting up libjsoncpp24:armhf (1.9.4-4) ...
Setting up zlib1g-dev:armhf (1:1.2.11.dfsg-2) ...
Setting up libnuma1:armhf (2.0.12-1) ...
Setting up libmd0:armhf (1.0.3-3) ...
Setting up libmpich12:armhf (3.4.1-3) ...
Setting up ocl-icd-libopencl1:armhf (2.2.14-2) ...
Setting up librhash0:armhf (1.4.1-1) ...
Setting up libuchardet0:armhf (0.0.7-1) ...
Setting up libnl-3-200:armhf (3.4.0-1) ...
Setting up libmpdec3:armhf (2.5.1-1+rpi1) ...
Setting up openmpi-common (4.1.0-8+rpi1) ...
Setting up libsub-override-perl (0.09-2) ...
Setting up libgfortran-10-dev:armhf (10.2.1-6+rpi1) ...
Setting up libssh2-1:armhf (1.9.0-2) ...
Setting up xorg-sgml-doctools (1:1.11-1.1) ...
Setting up cmake-data (3.18.4-2+rpi1) ...
Setting up libboost-dev:armhf (1.74.0.3+b1) ...
Setting up libjs-jquery (3.5.1+dfsg+~3.5.5-7) ...
Setting up libfido2-1:armhf (1.6.0-2) ...
Setting up libbsd0:armhf (0.11.3-1) ...
Setting up libelf1:armhf (0.183-1) ...
Setting up libxml2:armhf (2.9.10+dfsg-6.3) ...
Setting up chrpath (0.16-2) ...
Setting up libprocps8:armhf (2:3.3.17-5) ...
Setting up libblas-dev:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so to provide /usr/lib/arm-linux-gnueabihf/libblas.so (libblas.so-arm-linux-gnueabihf) in auto mode
Setting up libpython3.9-stdlib:armhf (3.9.2-1+rpi1) ...
Setting up libpython3-stdlib:armhf (3.9.2-2) ...
Setting up libevent-pthreads-2.1-7:armhf (2.1.12-stable-1) ...
Setting up x11proto-dev (2020.1-1) ...
Setting up libfile-stripnondeterminism-perl (1.11.0-1) ...
Setting up libxdmcp6:armhf (1:1.1.2-3) ...
Setting up libevent-extra-2.1-7:armhf (2.1.12-stable-1) ...
Setting up liblapack3:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode
Setting up libxcb1:armhf (1.14-3) ...
Setting up gettext (0.21-4) ...
Setting up libxau-dev:armhf (1:1.0.9-1) ...
Setting up libtool (2.4.6-15) ...
Setting up libarchive13:armhf (3.4.3-2) ...
Setting up libfftw3-bin (3.3.8-2) ...
Setting up libedit2:armhf (3.1-20191231-2) ...
Setting up hwloc-nox (2.4.1+dfsg-1) ...
Setting up libevent-openssl-2.1-7:armhf (2.1.12-stable-1) ...
Setting up m4 (1.4.18-5) ...
Setting up intltool-debian (0.35.0+20060710.5) ...
Setting up libnuma-dev:armhf (2.0.12-1) ...
Setting up libnl-route-3-200:armhf (3.4.0-1) ...
Setting up libxdmcp-dev:armhf (1:1.1.2-3) ...
Setting up libjs-jquery-ui (1.12.1+dfsg-8) ...
Setting up libevent-dev (2.1.12-stable-1) ...
Setting up liblapack-dev:armhf (3.9.0-3) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so to provide /usr/lib/arm-linux-gnueabihf/liblapack.so (liblapack.so-arm-linux-gnueabihf) in auto mode
Setting up gfortran-10 (10.2.1-6+rpi1) ...
Setting up autoconf (2.69-14) ...
Setting up dh-strip-nondeterminism (1.11.0-1) ...
Setting up dwz (0.13+20210201-1) ...
Setting up libnl-3-dev:armhf (3.4.0-1) ...
Setting up groff-base (1.22.4-6) ...
Setting up procps (2:3.3.17-5) ...
Setting up libcurl4:armhf (7.74.0-1.2) ...
Setting up libx11-6:armhf (2:1.7.0-2) ...
Setting up libfftw3-dev:armhf (3.3.8-2) ...
Setting up python3.9 (3.9.2-1+rpi1) ...
Setting up automake (1:1.16.3-2) ...
update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode
Setting up libibverbs1:armhf (33.1-1) ...
Setting up libxcb1-dev:armhf (1.14-3) ...
Setting up ibverbs-providers:armhf (33.1-1) ...
Setting up mpich (3.4.1-3) ...
update-alternatives: using /usr/bin/mpicc.mpich to provide /usr/bin/mpicc (mpi) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/mpicc.1.gz because associated file /usr/share/man/man1/mpicc.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpic++.1.gz because associated file /usr/share/man/man1/mpicxx.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpicxx.1.gz because associated file /usr/share/man/man1/mpicxx.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpiCC.1.gz because associated file /usr/share/man/man1/mpicxx.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpif77.1.gz because associated file /usr/share/man/man1/mpif77.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpif90.1.gz because associated file /usr/share/man/man1/mpif90.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpifort.1.gz because associated file /usr/share/man/man1/mpifort.mpich.1.gz (of link group mpi) doesn't exist
update-alternatives: using /usr/bin/mpirun.mpich to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: warning: skip creation of /usr/share/man/man1/mpirun.1.gz because associated file /usr/share/man/man1/mpirun.mpich.1.gz (of link group mpirun) doesn't exist
update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.mpich.1.gz (of link group mpirun) doesn't exist
Setting up openssh-client (1:8.4p1-5) ...
Setting up po-debconf (1.0.21+nmu1) ...
Setting up libx11-dev:armhf (2:1.7.0-2) ...
Setting up libxext6:armhf (2:1.3.3-1.1) ...
Setting up python3 (3.9.2-2) ...
Setting up man-db (2.9.4-2) ...
Not building database; man-db/auto-update is not 'true'.
Setting up gfortran (4:10.2.1-1+rpi1) ...
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode
update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode
Setting up libxnvctrl0:armhf (460.56-1) ...
Setting up dh-autoreconf (20) ...
Setting up libnl-route-3-dev:armhf (3.4.0-1) ...
Setting up libltdl-dev:armhf (2.4.6-15) ...
Setting up libmpich-dev:armhf (3.4.1-3) ...
Setting up cmake (3.18.4-2+rpi1) ...
Setting up libhwloc-dev:armhf (2.4.1+dfsg-1) ...
Setting up lsb-release (11.1.0+rpi1) ...
Setting up librdmacm1:armhf (33.1-1) ...
Setting up debhelper (13.3.4) ...
Setting up libibverbs-dev:armhf (33.1-1) ...
Setting up libhwloc-plugins:armhf (2.4.1+dfsg-1) ...
Setting up libfabric1 (1.11.0-2) ...
Setting up libpmix2:armhf (4.0.0-4) ...
Setting up libopenmpi3:armhf (4.1.0-8+rpi1) ...
Setting up libpmix-dev:armhf (4.0.0-4) ...
Setting up openmpi-bin (4.1.0-8+rpi1) ...
update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode
update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode
Setting up libopenmpi-dev:armhf (4.1.0-8+rpi1) ...
update-alternatives: using /usr/lib/arm-linux-gnueabihf/openmpi/include to provide /usr/include/arm-linux-gnueabihf/mpi (mpi-arm-linux-gnueabihf) in auto mode
Setting up sbuild-build-depends-gromacs-dummy (0.invalid.0) ...
Processing triggers for libc-bin (2.31-10+rpi1) ...
W: No sandbox user '_apt' on the system, can not drop privileges
+------------------------------------------------------------------------------+
| Build environment |
+------------------------------------------------------------------------------+
Kernel: Linux 4.9.0-0.bpo.6-armmp armhf (armv7l)
Toolchain package versions: binutils_2.35.2-2+rpi1 dpkg-dev_1.20.7.1+rpi1 g++-10_10.2.1-6+rpi1 gcc-10_10.2.1-6+rpi1 libc6-dev_2.31-10+rpi1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 linux-libc-dev_5.10.24-1+rpi1
Package versions: adduser_3.118 apt_2.2.2 autoconf_2.69-14 automake_1:1.16.3-2 autopoint_0.21-4 autotools-dev_20180224.1+nmu1 base-files_11+rpi1 base-passwd_3.5.49 bash_5.1-2 binutils_2.35.2-2+rpi1 binutils-arm-linux-gnueabihf_2.35.2-2+rpi1 binutils-common_2.35.2-2+rpi1 bsdextrautils_2.36.1-7 bsdutils_1:2.36.1-7 build-essential_12.9 bzip2_1.0.8-4 chrpath_0.16-2 cmake_3.18.4-2+rpi1 cmake-data_3.18.4-2+rpi1 coreutils_8.32-4 cpp_4:10.2.1-1+rpi1 cpp-10_10.2.1-6+rpi1 dash_0.5.11+git20200708+dd9ef66-5 debconf_1.5.75 debhelper_13.3.4 debianutils_4.11.2 dh-autoreconf_20 dh-strip-nondeterminism_1.11.0-1 diffutils_1:3.7-5 dirmngr_2.2.27-1 distro-info-data_0.46 dpkg_1.20.7.1+rpi1 dpkg-dev_1.20.7.1+rpi1 dwz_0.13+20210201-1 e2fsprogs_1.46.2-1 fakeroot_1.25.3-1.1 fdisk_2.36.1-7 file_1:5.39-3 findutils_4.8.0-1 g++_4:10.2.1-1+rpi1 g++-10_10.2.1-6+rpi1 gcc_4:10.2.1-1+rpi1 gcc-10_10.2.1-6+rpi1 gcc-10-base_10.2.1-6+rpi1 gettext_0.21-4 gettext-base_0.21-4 gfortran_4:10.2.1-1+rpi1 gfortran-10_10.2.1-6+rpi1 gnupg_2.2.27-1 gnupg-l10n_2.2.27-1 gnupg-utils_2.2.27-1 gpg_2.2.27-1 gpg-agent_2.2.27-1 gpg-wks-client_2.2.27-1 gpg-wks-server_2.2.27-1 gpgconf_2.2.27-1 gpgsm_2.2.27-1 gpgv_2.2.27-1 grep_3.6-1 groff-base_1.22.4-6 gzip_1.10-4 hostname_3.23 hwloc-nox_2.4.1+dfsg-1 ibverbs-providers_33.1-1 init-system-helpers_1.60 intltool-debian_0.35.0+20060710.5 iputils-ping_3:20210202-1 libacl1_2.2.53-10 libapt-pkg6.0_2.2.2 libarchive-zip-perl_1.68-1 libarchive13_3.4.3-2 libasan6_10.2.1-6+rpi1 libassuan0_2.5.3-7.1 libatomic1_10.2.1-6+rpi1 libattr1_1:2.4.48-6 libaudit-common_1:3.0-2 libaudit1_1:3.0-2 libbinutils_2.35.2-2+rpi1 libblas-dev_3.9.0-3 libblas3_3.9.0-3 libblkid1_2.36.1-7 libboost-dev_1.74.0.3+b1 libboost1.74-dev_1.74.0-9 libbrotli1_1.0.9-2+b1 libbsd0_0.11.3-1 libbz2-1.0_1.0.8-4 libc-bin_2.31-10+rpi1 libc-dev-bin_2.31-10+rpi1 libc6_2.31-10+rpi1 libc6-dev_2.31-10+rpi1 libcap-ng0_0.7.9-2.2+b1 libcap2_1:2.44-1 libcap2-bin_1:2.44-1 libcbor0_0.5.0+dfsg-2 libcc1-0_10.2.1-6+rpi1 libcom-err2_1.46.2-1 libcrypt-dev_1:4.4.17-1 libcrypt1_1:4.4.17-1 libctf-nobfd0_2.35.2-2+rpi1 libctf0_2.35.2-2+rpi1 libcurl4_7.74.0-1.2 libdb5.3_5.3.28+dfsg1-0.8 libdebconfclient0_0.256 libdebhelper-perl_13.3.4 libdpkg-perl_1.20.7.1+rpi1 libedit2_3.1-20191231-2 libelf1_0.183-1 libevent-2.1-7_2.1.12-stable-1 libevent-core-2.1-7_2.1.12-stable-1 libevent-dev_2.1.12-stable-1 libevent-extra-2.1-7_2.1.12-stable-1 libevent-openssl-2.1-7_2.1.12-stable-1 libevent-pthreads-2.1-7_2.1.12-stable-1 libexpat1_2.2.10-2 libext2fs2_1.46.2-1 libfabric1_1.11.0-2 libfakeroot_1.25.3-1.1 libfdisk1_2.36.1-7 libffi7_3.3-6 libfftw3-bin_3.3.8-2 libfftw3-dev_3.3.8-2 libfftw3-double3_3.3.8-2 libfftw3-single3_3.3.8-2 libfido2-1_1.6.0-2 libfile-stripnondeterminism-perl_1.11.0-1 libgcc-10-dev_10.2.1-6+rpi1 libgcc-s1_10.2.1-6+rpi1 libgcrypt20_1.8.7-3 libgdbm-compat4_1.19-2 libgdbm6_1.19-2 libgfortran-10-dev_10.2.1-6+rpi1 libgfortran5_10.2.1-6+rpi1 libgmp10_2:6.2.1+dfsg-1 libgnutls30_3.7.1-1 libgomp1_10.2.1-6+rpi1 libgpg-error0_1.38-2 libgssapi-krb5-2_1.18.3-4 libhogweed6_3.7-2.1 libhwloc-dev_2.4.1+dfsg-1 libhwloc-plugins_2.4.1+dfsg-1 libhwloc15_2.4.1+dfsg-1 libibverbs-dev_33.1-1 libibverbs1_33.1-1 libicu67_67.1-6 libidn2-0_2.3.0-5 libisl23_0.23-1 libjs-jquery_3.5.1+dfsg+~3.5.5-7 libjs-jquery-ui_1.12.1+dfsg-8 libjsoncpp24_1.9.4-4 libk5crypto3_1.18.3-4 libkeyutils1_1.6.1-2 libkrb5-3_1.18.3-4 libkrb5support0_1.18.3-4 libksba8_1.5.0-3 liblapack-dev_3.9.0-3 liblapack3_3.9.0-3 libldap-2.4-2_2.4.57+dfsg-2 libldap-common_2.4.57+dfsg-2 libltdl-dev_2.4.6-15 libltdl7_2.4.6-15 liblz4-1_1.9.3-1+rpi1 liblzma5_5.2.5-2 libmagic-mgc_1:5.39-3 libmagic1_1:5.39-3 libmd0_1.0.3-3 libmount1_2.36.1-7 libmpc3_1.2.0-1 libmpdec3_2.5.1-1+rpi1 libmpfr6_4.1.0-3 libmpich-dev_3.4.1-3 libmpich12_3.4.1-3 libncurses6_6.2+20201114-2 libncursesw6_6.2+20201114-2 libnettle8_3.7-2.1 libnghttp2-14_1.43.0-1 libnl-3-200_3.4.0-1 libnl-3-dev_3.4.0-1 libnl-route-3-200_3.4.0-1 libnl-route-3-dev_3.4.0-1 libnpth0_1.6-3 libnsl-dev_1.3.0-2 libnsl2_1.3.0-2 libnss-nis_3.1-4 libnss-nisplus_1.3-4 libnuma-dev_2.0.12-1 libnuma1_2.0.12-1 libopenmpi-dev_4.1.0-8+rpi1 libopenmpi3_4.1.0-8+rpi1 libp11-kit0_0.23.22-1 libpam-cap_1:2.44-1 libpam-modules_1.4.0-7 libpam-modules-bin_1.4.0-7 libpam-runtime_1.4.0-7 libpam0g_1.4.0-7 libpciaccess0_0.16-1 libpcre2-8-0_10.36-2 libpcre3_2:8.39-13 libperl5.32_5.32.1-3 libpipeline1_1.5.3-1 libpmix-dev_4.0.0-4 libpmix2_4.0.0-4 libprocps8_2:3.3.17-5 libpsl5_0.21.0-1.2 libpthread-stubs0-dev_0.4-1 libpython3-stdlib_3.9.2-2 libpython3.9-minimal_3.9.2-1+rpi1 libpython3.9-stdlib_3.9.2-1+rpi1 librdmacm1_33.1-1 libreadline8_8.1-1 librhash0_1.4.1-1 librtmp1_2.4+20151223.gitfa8646d.1-2+b2 librust-rand-core-dev_0.5.1-1 libsasl2-2_2.1.27+dfsg-2.1 libsasl2-modules-db_2.1.27+dfsg-2.1 libseccomp2_2.5.1-1+rpi1 libselinux1_3.1-3 libsemanage-common_3.1-1 libsemanage1_3.1-1+b1 libsepol1_3.1-1 libsigsegv2_2.13-1 libslurm36_20.11.4-1 libsmartcols1_2.36.1-7 libsqlite3-0_3.34.1-3 libss2_1.46.2-1 libssh2-1_1.9.0-2 libssl1.1_1.1.1k-1 libstdc++-10-dev_10.2.1-6+rpi1 libstdc++6_10.2.1-6+rpi1 libsub-override-perl_0.09-2 libsystemd0_247.3-1+rpi1 libtasn1-6_4.16.0-2 libtinfo6_6.2+20201114-2 libtirpc-common_1.3.1-1 libtirpc-dev_1.3.1-1 libtirpc3_1.3.1-1 libtool_2.4.6-15 libubsan1_10.2.1-6+rpi1 libuchardet0_0.0.7-1 libudev1_247.3-1+rpi1 libunistring2_0.9.10-4 libuuid1_2.36.1-7 libuv1_1.40.0-1 libx11-6_2:1.7.0-2 libx11-data_2:1.7.0-2 libx11-dev_2:1.7.0-2 libxau-dev_1:1.0.9-1 libxau6_1:1.0.9-1 libxcb1_1.14-3 libxcb1-dev_1.14-3 libxdmcp-dev_1:1.1.2-3 libxdmcp6_1:1.1.2-3 libxext6_2:1.3.3-1.1 libxml2_2.9.10+dfsg-6.3 libxnvctrl0_460.56-1 libxxhash0_0.8.0-2+rpi1 libzstd1_1.4.8+dfsg-2.1 linux-libc-dev_5.10.24-1+rpi1 login_1:4.8.1-1 logsave_1.46.2-1 lsb-base_11.1.0+rpi1 lsb-release_11.1.0+rpi1 m4_1.4.18-5 make_4.3-4 man-db_2.9.4-2 mawk_1.3.4.20200120-2 media-types_4.0.0 mount_2.36.1-7 mpich_3.4.1-3 ncurses-base_6.2+20201114-2 ncurses-bin_6.2+20201114-2 netbase_6.2 ocl-icd-libopencl1_2.2.14-2 openmpi-bin_4.1.0-8+rpi1 openmpi-common_4.1.0-8+rpi1 openssh-client_1:8.4p1-5 passwd_1:4.8.1-1 patch_2.7.6-7 perl_5.32.1-3 perl-base_5.32.1-3 perl-modules-5.32_5.32.1-3 pinentry-curses_1.1.0-4 po-debconf_1.0.21+nmu1 procps_2:3.3.17-5 python3_3.9.2-2 python3-minimal_3.9.2-2 python3.9_3.9.2-1+rpi1 python3.9-minimal_3.9.2-1+rpi1 raspbian-archive-keyring_20120528.2 readline-common_8.1-1 sbuild-build-depends-core-dummy_0.invalid.0 sbuild-build-depends-gromacs-dummy_0.invalid.0 sed_4.7-1 sensible-utils_0.0.14 sysvinit-utils_2.96-6 tar_1.34+dfsg-1 tzdata_2021a-1 util-linux_2.36.1-7 x11proto-dev_2020.1-1 xorg-sgml-doctools_1:1.11-1.1 xtrans-dev_1.4.0-1 xz-utils_5.2.5-2 zlib1g_1:1.2.11.dfsg-2 zlib1g-dev_1:1.2.11.dfsg-2
+------------------------------------------------------------------------------+
| Build |
+------------------------------------------------------------------------------+
Unpack source
-------------
gpgv: unknown type of key resource 'trustedkeys.kbx'
gpgv: keyblock resource '/tmp/dpkg-verify-sig.qLvzNCMx/trustedkeys.kbx': General error
gpgv: Signature made Mon Mar 29 05:23:05 2021 UTC
gpgv: using RSA key 843E5FA61E6063389876D2E5EE4AFD69EC65108F
gpgv: issuer "nbreen@debian.org"
gpgv: Can't check signature: No public key
dpkg-source: warning: failed to verify signature on ./gromacs_2020.6-2.dsc
dpkg-source: info: extracting gromacs in /<<PKGBUILDDIR>>
dpkg-source: info: unpacking gromacs_2020.6.orig.tar.gz
dpkg-source: info: unpacking gromacs_2020.6.orig-regressiontests.tar.gz
dpkg-source: info: unpacking gromacs_2020.6-2.debian.tar.xz
dpkg-source: info: using patch list from debian/patches/series
dpkg-source: info: applying disable-listed-forces-test.patch
dpkg-source: info: applying arm64-disable-numa-test.patch
dpkg-source: info: applying readme.patch
dpkg-source: info: applying copyright-file.patch
dpkg-source: info: applying disable-cpuinfotest.patch
dpkg-source: info: applying mdrun-test-timeout.patch
dpkg-source: info: applying local-mathjax.patch
dpkg-source: info: applying mpi-tests-localhost.patch
Check disc space
----------------
Sufficient free space for build
User Environment
----------------
APT_CONFIG=/var/lib/sbuild/apt.conf
DEB_BUILD_OPTIONS=parallel=4
HOME=/sbuild-nonexistent
LC_ALL=POSIX
LOGNAME=buildd
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games
SCHROOT_ALIAS_NAME=bullseye-staging-armhf-sbuild
SCHROOT_CHROOT_NAME=bullseye-staging-armhf-sbuild
SCHROOT_COMMAND=env
SCHROOT_GID=109
SCHROOT_GROUP=buildd
SCHROOT_SESSION_ID=bullseye-staging-armhf-sbuild-5e2b5fa6-7c6d-42dc-9882-dae9be53cd7f
SCHROOT_UID=104
SCHROOT_USER=buildd
SHELL=/bin/sh
TERM=linux
USER=buildd
dpkg-buildpackage
-----------------
dpkg-buildpackage: info: source package gromacs
dpkg-buildpackage: info: source version 2020.6-2
dpkg-buildpackage: info: source distribution unstable
dpkg-source --before-build .
dpkg-buildpackage: info: host architecture armhf
debian/rules clean
dh_testdir
dh_testroot
rm -rf build docs/doxygen/*.pyc
dh_clean build-basic build-mpich build-openmpi build-manual configure-stamp \
debian/gromacs-mpich.README.Debian debian/gromacs-openmpi.README.Debian
debian/rules binary-arch
dh_testdir
(mkdir -p build/basic; cd build/basic; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_INSTALL_LEGACY_API=ON)
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: ""
-- Using default library suffix: ""
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic
(mkdir -p build/basic-dp; cd build/basic-dp; cmake /<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=OFF -DGMX_X11=ON -DBUILD_SHARED_LIBS=ON -DGMX_DOUBLE=ON)
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/cc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5")
-- Found X11: /usr/include
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so
-- Looking for XOpenDisplay in /usr/lib/arm-linux-gnueabihf/libX11.so - found
-- Looking for gethostbyname
-- Looking for gethostbyname - found
-- Looking for connect
-- Looking for connect - found
-- Looking for remove
-- Looking for remove - found
-- Looking for shmat
-- Looking for shmat - found
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- Using dynamic plugins (e.g VMD-supported file formats)
-- Checking for suitable VMD version
-- VMD plugins not found. Path to VMD can be set with VMDDIR.
-- Using default binary suffix: "_d"
-- Using default library suffix: "_d"
-- Could not convert sample image, ImageMagick convert can not be used. A possible way to fix it can be found here: https://alexvanderbist.com/2018/fixing-imagick-error-unauthorized
Traceback (most recent call last):
File "<string>", line 1, in <module>
ModuleNotFoundError: No module named 'pygments'
-- Could NOT find Sphinx (missing: SPHINX_EXECUTABLE pygments) (Required is at least version "1.6.1")
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Could NOT find Doxygen (missing: DOXYGEN_EXECUTABLE)
-- Doxygen not found. Documentation targets will not be generated.
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/basic-dp
(mkdir -p build/mpich; cd build/mpich; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.mpich" -DGMX_LIBS_SUFFIX="_mpi.mpich")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.mpich - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.mpich"
-- Using manually set library suffix: "_mpi.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich
(mkdir -p build/mpich-dp; cd build/mpich-dp; CC=/usr/bin/mpicc.mpich CXX=/usr/bin/mpicxx.mpich cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DMPIEXEC="/usr/bin/mpiexec.mpich" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.mpich" -DGMX_LIBS_SUFFIX="_mpi_d.mpich")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.mpich - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.mpich - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.mpich"
-- Using manually set library suffix: "_mpi_d.mpich"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/mpich-dp
(mkdir -p build/openmpi; cd build/openmpi; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_BINARY_SUFFIX="_mpi.openmpi" -DGMX_LIBS_SUFFIX="_mpi.openmpi")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Looking for NVIDIA GPUs present in the system
-- Could not detect NVIDIA GPUs
-- No compatible CUDA toolkit found (v5.0+), disabling native GPU acceleration
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3f, trying generic detection
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - not found
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so
-- Looking for fftwf_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3f.so - found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi.openmpi"
-- Using manually set library suffix: "_mpi.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi
(mkdir -p build/openmpi-dp; cd build/openmpi-dp; CC=/usr/bin/mpicc.openmpi CXX=/usr/bin/mpicxx.openmpi cmake \
/<<PKGBUILDDIR>> -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_RULE_MESSAGES=OFF -DCMAKE_INSTALL_PREFIX="/usr" -DCMAKE_EXE_LINKER_FLAGS="-Wl,-z,relro -Wl,-z,now" -DCMAKE_SKIP_RPATH=ON -DGMX_EXTERNAL_ZLIB=ON -DGMX_VERSION_STRING_OF_FORK="Raspbian-2020.6-2" -DGMX_GIT_VERSION_INFO=OFF -DGMX_SIMD=None -DGMX_MPI=ON -DGMX_X11=OFF -DGMX_DEFAULT_SUFFIX=OFF -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib/openmpi/lib -Wl,-z,relro -Wl,-z,now" -DMPIEXEC="/usr/bin/mpiexec.openmpi" -DGMX_BUILD_MDRUN_ONLY=ON -DGMX_DOUBLE=ON -DGMX_BINARY_SUFFIX="_mpi_d.openmpi" -DGMX_LIBS_SUFFIX="_mpi_d.openmpi")
-- The C compiler identification is GNU 10.2.1
-- The CXX compiler identification is GNU 10.2.1
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /usr/bin/mpicc.openmpi - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/mpicxx.openmpi - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
CMake Warning at cmake/gmxManageGPU.cmake:53 (message):
GPU acceleration is not available in double precision, disabled!
Call Stack (most recent call first):
CMakeLists.txt:217 (include)
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Performing Test CFLAGS_EXCESS_PREC
-- Performing Test CFLAGS_EXCESS_PREC - Success
-- Performing Test CFLAGS_COPT
-- Performing Test CFLAGS_COPT - Success
-- Performing Test CFLAGS_NOINLINE
-- Performing Test CFLAGS_NOINLINE - Success
-- Performing Test CXXFLAGS_EXCESS_PREC
-- Performing Test CXXFLAGS_EXCESS_PREC - Success
-- Performing Test CXXFLAGS_COPT
-- Performing Test CXXFLAGS_COPT - Success
-- Performing Test CXXFLAGS_NOINLINE
-- Performing Test CXXFLAGS_NOINLINE - Success
-- Looking for include file unistd.h
-- Looking for include file unistd.h - found
-- Looking for include file pwd.h
-- Looking for include file pwd.h - found
-- Looking for include file dirent.h
-- Looking for include file dirent.h - found
-- Looking for include file time.h
-- Looking for include file time.h - found
-- Looking for include file sys/time.h
-- Looking for include file sys/time.h - found
-- Looking for include file io.h
-- Looking for include file io.h - not found
-- Looking for include file sched.h
-- Looking for include file sched.h - found
-- Looking for include file xmmintrin.h
-- Looking for include file xmmintrin.h - not found
-- Looking for gettimeofday
-- Looking for gettimeofday - found
-- Looking for sysconf
-- Looking for sysconf - found
-- Looking for nice
-- Looking for nice - found
-- Looking for fsync
-- Looking for fsync - found
-- Looking for _fileno
-- Looking for _fileno - not found
-- Looking for fileno
-- Looking for fileno - found
-- Looking for _commit
-- Looking for _commit - not found
-- Looking for sigaction
-- Looking for sigaction - found
-- Performing Test HAVE_BUILTIN_CLZ
-- Performing Test HAVE_BUILTIN_CLZ - Success
-- Performing Test HAVE_BUILTIN_CLZLL
-- Performing Test HAVE_BUILTIN_CLZLL - Success
-- Looking for clock_gettime in rt
-- Looking for clock_gettime in rt - found
-- Looking for feenableexcept in m
-- Looking for feenableexcept in m - found
-- Looking for fedisableexcept in m
-- Looking for fedisableexcept in m - found
-- Checking for sched.h GNU affinity API
-- Performing Test sched_affinity_compile
-- Performing Test sched_affinity_compile - Success
-- Looking for include file mm_malloc.h
-- Looking for include file mm_malloc.h - not found
-- Looking for include file malloc.h
-- Looking for include file malloc.h - found
-- Checking for _mm_malloc()
-- Checking for _mm_malloc() - not supported
-- Looking for posix_memalign
-- Looking for posix_memalign - found
-- Looking for memalign
-- Looking for memalign - not found
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- MPI is not compatible with thread-MPI. Disabling thread-MPI.
-- Checking for MPI_IN_PLACE
-- Performing Test MPI_IN_PLACE_COMPILE_OK
-- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
-- Checking for MPI_IN_PLACE - yes
-- Defaulting to building static libraries
-- Looking for HWLOC
-- Looking for hwloc_topology_init
-- Looking for hwloc_topology_init - found
-- hwloc version:
-- Found HWLOC: /usr/lib/arm-linux-gnueabihf/libhwloc.so (found suitable version "2.4.1", minimum required is "1.5")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success
-- Found Threads: TRUE
-- Looking for C++ include pthread.h
-- Looking for C++ include pthread.h - found
-- Atomic operations found
-- Performing Test PTHREAD_SETAFFINITY
-- Performing Test PTHREAD_SETAFFINITY - Success
-- Found ZLIB: /usr/lib/arm-linux-gnueabihf/libz.so (found version "1.2.11")
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so
-- Looking for zlibVersion in /usr/lib/arm-linux-gnueabihf/libz.so - found
-- Checking for GCC x86 inline asm
-- Checking for GCC x86 inline asm - not supported
-- Detected build CPU vendor - ARM
-- Detected build CPU brand - ARMv7 Processor rev 10 (v7l)
-- Detected build CPU family - 7
-- Detected build CPU model - 2
-- Detected build CPU stepping - 10
-- Detected build CPU features - neon
-- Disabling RDTSCP support
-- Checking for 64-bit off_t
-- Checking for 64-bit off_t - present with _FILE_OFFSET_BITS=64
-- Checking for fseeko/ftello
-- Checking for fseeko/ftello - present
-- Checking for SIGUSR1
-- Checking for SIGUSR1 - found
-- Checking for pipe support
-- Checking for system XDR support
-- Checking for system XDR support - present
-- SIMD instructions disabled
-- Performing Test _callconv___vectorcall
-- Performing Test _callconv___vectorcall - Failed
-- Performing Test _callconv___regcall
-- Performing Test _callconv___regcall - Failed
-- Performing Test _callconv_
-- Performing Test _callconv_ - Success
-- pkg-config could not detect fftw3, trying generic detection
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_r2c in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_plan_many_dft_c2r in /usr/lib/arm-linux-gnueabihf/libfftw3.so - found
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_sse2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx2_128 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_128_fma in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_avx_512 in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_kcvi in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_neon in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_vsx in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_simd_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so
-- Looking for fftw_have_altivec in /usr/lib/arm-linux-gnueabihf/libfftw3.so - not found
-- Using external FFT library - FFTW3
-- Looking for sgemm_
-- Looking for sgemm_ - not found
-- Looking for sgemm_
-- Looking for sgemm_ - found
-- Found BLAS: /usr/lib/arm-linux-gnueabihf/libblas.so
-- Looking for cheev_
-- Looking for cheev_ - not found
-- Looking for cheev_
-- Looking for cheev_ - found
-- A library with LAPACK API found.
-- Checking for dlopen
-- Performing Test HAVE_DLOPEN
-- Performing Test HAVE_DLOPEN - Success
-- Checking for dlopen - found
-- GROMACS only supports plugins in a build that uses shared libraries, which can be disabled for various reasons. BUILD_SHARED_LIBS=on and a toolchain that supports dynamic linking is required. (Hint: GMX_PREFER_STATIC_LIBS and GMX_BUILD_MDRUN_ONLY can influence the default BUILD_SHARED_LIBS, so if you need plugins, reconsider those choices.)
-- Not using dynamic plugins (e.g VMD-supported file formats)
-- Using manually set binary suffix: "_mpi_d.openmpi"
-- Using manually set library suffix: "_mpi_d.openmpi"
-- Performing Test HAVE_NO_DEPRECATED_COPY
-- Performing Test HAVE_NO_DEPRECATED_COPY - Success
-- Performing Test HAS_NO_STRINGOP_TRUNCATION
-- Performing Test HAS_NO_STRINGOP_TRUNCATION - Success
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION
-- Performing Test HAS_NO_UNUSED_MEMBER_FUNCTION - Success
-- Performing Test HAS_NO_REDUNDANT_MOVE
-- Performing Test HAS_NO_REDUNDANT_MOVE - Success
-- Performing Test HAS_NO_UNUSED
-- Performing Test HAS_NO_UNUSED - Success
-- Performing Test HAS_NO_UNUSED_PARAMETER
-- Performing Test HAS_NO_UNUSED_PARAMETER - Success
-- Performing Test HAS_NO_MISSING_DECLARATIONS
-- Performing Test HAS_NO_MISSING_DECLARATIONS - Success
-- Performing Test HAS_NO_NULL_CONVERSIONS
-- Performing Test HAS_NO_NULL_CONVERSIONS - Success
-- Performing Test HAS_NO_CLASS_MEMACCESS
-- Performing Test HAS_NO_CLASS_MEMACCESS - Success
-- Check if the system is big endian
-- Searching 16 bit integer
-- Searching 16 bit integer - Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Configuring done
-- Generating done
-- Build files have been written to: /<<PKGBUILDDIR>>/build/openmpi-dp
touch configure-stamp
dh_testdir
/usr/bin/make -j4 -C build/basic
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles /<<PKGBUILDDIR>>/build/basic//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Raspbian-2020.6-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.6-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
Scanning dependencies of target scanner
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
Scanning dependencies of target thread_mpi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
[ 0%] Built target release-version-info
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
[ 0%] Built target lmfit_objlib
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 1%] Built target scanner
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target thread_mpi
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
Scanning dependencies of target vmddlopen
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target vmddlopen
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target view_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 7%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 10%] Built target view_objlib
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2293 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs.so.5 -o ../../lib/libgromacs.so.5.0.0 CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o CMakeFiles/libgromacs.dir/utility/futil.cpp.o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o CMakeFiles/libgromacs.dir/utility/init.cpp.o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o CMakeFiles/libgromacs.dir/utility/logger.cpp.o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o CMakeFiles/libgromacs.dir/utility/path.cpp.o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o CMakeFiles/libgromacs.dir/math/functions.cpp.o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o CMakeFiles/libgromacs.dir/math/units.cpp.o CMakeFiles/libgromacs.dir/math/utilities.cpp.o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o CMakeFiles/libgromacs.dir/random/seed.cpp.o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o CMakeFiles/libgromacs.dir/topology/block.cpp.o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o CMakeFiles/libgromacs.dir/topology/idef.cpp.o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o CMakeFiles/libgromacs.dir/topology/index.cpp.o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o CMakeFiles/libgromacs.dir/topology/topology.cpp.o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o CMakeFiles/libgromacs.dir/pulling/output.cpp.o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o CMakeFiles/libgromacs.dir/awh/awh.cpp.o CMakeFiles/libgromacs.dir/awh/bias.cpp.o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o CMakeFiles/libgromacs.dir/awh/grid.cpp.o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o CMakeFiles/libgromacs.dir/simd/support.cpp.o CMakeFiles/libgromacs.dir/imd/imd.cpp.o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o CMakeFiles/libgromacs.dir/tools/check.cpp.o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o CMakeFiles/libgromacs.dir/tools/dump.cpp.o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o CMakeFiles/libgromacs.dir/fft/fft.cpp.o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o CMakeFiles/libgromacs.dir/options/options.cpp.o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o CMakeFiles/libgromacs.dir/selection/params.cpp.o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o CMakeFiles/libgromacs.dir/selection/position.cpp.o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o CMakeFiles/libgromacs.dir/selection/selection.cpp.o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/energyelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o fileio/CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs.so.5.0.0 ../../lib/libgromacs.so.5 ../../lib/libgromacs.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target libgromacs
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/depend
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/share/template /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/share/template /<<PKGBUILDDIR>>/build/basic/share/template/CMakeFiles/template.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp /<<PKGBUILDDIR>>/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
Scanning dependencies of target gmx
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
Scanning dependencies of target template
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f share/template/CMakeFiles/template.dir/build.make share/template/CMakeFiles/template.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/c++ -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -std=c++14 -o CMakeFiles/template.dir/template.cpp.o -c /<<PKGBUILDDIR>>/share/template/template.cpp
Scanning dependencies of target gmxapi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx ../../lib/libgromacs.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/share/template && /usr/bin/cmake -E cmake_link_script CMakeFiles/template.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/template.dir/template.cpp.o -o ../../bin/template ../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 98%] Built target template
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi.so.0 -o ../../../lib/libgmxapi.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi.so.0.1.0 ../../../lib/libgmxapi.so.0 ../../../lib/libgmxapi.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target gmxapi
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -j4 -C build/basic-dp
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles /<<PKGBUILDDIR>>/build/basic-dp//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Raspbian-2020.6-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.6-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
Scanning dependencies of target scanner
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
Scanning dependencies of target thread_mpi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
[ 0%] Built target release-version-info
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/alltoall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_protocol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/barrier.cpp
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_send_recv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/bcast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/p2p_wait.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/collective.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/profile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/comm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 1%] Built target lmfit_objlib
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/event.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/reduce_fast.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scatter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/list.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/type.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 1%] Built target scanner
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/scan.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/numa_malloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/once.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target thread_mpi
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
Scanning dependencies of target vmddlopen
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio && /usr/bin/c++ -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o -c /<<PKGBUILDDIR>>/src/external/vmd_molfile/vmddlopen.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target vmddlopen
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/view_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target view_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/view_objlib.dir/build.make src/programs/CMakeFiles/view_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/3dview.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/3dview.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/buttons.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/buttons.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cc -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/basic-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/dialogs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/fgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/filter.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/logo.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/logo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:68:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
68 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/manager.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp: In function 'bool ManCallBack(t_x11*, XEvent*, Window, void*)':
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
366 | put_atoms_in_compact_unitcell(man->molw->ePBC, ecenterDEF, man->box, atomsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/programs/view/manager.cpp:366:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/molps.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/molps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nleg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nleg.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/nmol.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/nmol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/popup.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/popup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/pulldown.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 6%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/view.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/view.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/x11.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/x11.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlg.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlghi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xdlgitem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xmb.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xmb.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -c /<<PKGBUILDDIR>>/src/programs/view/xutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 9%] Built target view_objlib
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::_ZN3gmx19StatePropagatorData24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 10%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1027:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1027 | fillCell(gridSetData, nbat, atomOffsetCell, atomOffsetCell + numAtomsCell, atinfo, x, nullptr);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1151:29: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1151 | fillCell(gridSetData, nbat, atomOffsetX, atomOffsetX + numAtomsX, atinfo, x,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1152 | bb_work_aligned);
| ~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:90:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
90 | nbnxn_put_on_grid(nbv, nullptr, zone, c0, c1, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
91 | { zones->cg_range[zone], zones->cg_range[zone + 1] }, -1, atomInfo, x, 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
92 | nullptr);
| ~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, tmpi_comm_* const*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
259 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
263 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
267 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:99:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
99 | impl_->scale(coordinates);
| ~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:163:21: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
163 | impl_->transform(coordinates);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2293 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:457:38: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
457 | calcUmbrellaForceAndPotential(dimParams, grid, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:481:42: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
481 | calcUmbrellaForceAndPotential(dimParams, grid, coordState_.umbrellaGridpoint(), newForce);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
242 | newHistogramSize = newHistogramSizeInitialStage(params, t, covered, weightsumCovering, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:242:56: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/anadih.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/angle_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/binsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/cmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dens_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/dlist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/eigio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/fitahx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_anaeig.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_analyze.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bar.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_bundle.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_awh.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_awh(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_chi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_confrms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_covar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_current.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_density.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_densorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dielectric.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dipoles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_mapping&}; _Tp = t_mapping; _Alloc = std::allocator<t_mapping>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_mapping>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'int strip_dssp(FILE*, int, const gmx_bool*, real, real*, FILE*, t_matrix*, int*, const gmx_output_env_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_do_dssp.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In function 'void prune_ss_legend(t_matrix*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_mapping*, std::vector<t_mapping> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dos.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_dyecoupl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_enemat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_filter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_gyrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_h2order.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hbond.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_helixorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_hydorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_lie.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_make_edi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mdmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmeig.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_msd.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In constructor 't_corr::t_corr(int, int, int, real, int, gmx_bool, gmx_bool, real, const t_topology*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmens.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_order.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'int gmx_nmtraj(int, char**)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_nmtraj.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_polystat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_potential.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_principal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rmsf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotacf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_rotmat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saltbr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sans.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_saxs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sigeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_sorient.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spatial.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_spol.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_tcaf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_trjorder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_vanhove.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_velacc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wham.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_wheel.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/hxprops.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void rainbow_map(gmx_bool, gmx::ArrayRef<t_mapping>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1328:13: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1328 | static void rainbow_map(gmx_bool bBlue, gmx::ArrayRef<t_mapping> map)
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void leg_continuous(t_psdata*, real, real, real, const string&, real, char*, gmx::ArrayRef<const t_mapping>, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:249:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
249 | static void leg_continuous(t_psdata* ps,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'void ps_mat(const char*, gmx::ArrayRef<t_matrix>, gmx::ArrayRef<t_matrix>, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool, int, real, real, real, const char*, const char*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
1033 | leg_continuous(&out, x0 + w / 2, w / 2, DDD, legend, psr->legfontsize, psr->legfont,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1034 | leg_map, mapoffset);
| ~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1033:31: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
316 | leg_continuous(ps, xx1, x1, y0, label1, fontsize, font, map1, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:316:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
317 | leg_continuous(ps, xx2, x2, y0, label2, fontsize, font, map2, 0);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:317:19: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nrama.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/nsfactor.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp: In function 'int gmx_xpm2ps(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/gmx_xpm2ps.cpp:1376:20: note: parameter passing for argument of type 'gmx::ArrayRef<t_mapping>' changed in GCC 7.1
1376 | rainbow_map(bBlue, m.map);
| ~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/powerspect.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/pp2shift.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/princ.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/sfactor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcZeroPointEnergy(gmx::ArrayRef<const double>, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:53:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
53 | double calcZeroPointEnergy(gmx::ArrayRef<const real> eigval, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalInternalEnergy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:66:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
66 | double calcVibrationalInternalEnergy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcVibrationalHeatCapacity(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:93:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | double calcVibrationalHeatCapacity(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool linear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcQuasiHarmonicEntropy(gmx::ArrayRef<const double>, real, gmx_bool, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:158:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
158 | double calcQuasiHarmonicEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear, real scale_factor)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp: In function 'double calcSchlitterEntropy(gmx::ArrayRef<const double>, real, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.cpp:185:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
185 | double calcSchlitterEntropy(gmx::ArrayRef<const real> eigval, real temperature, gmx_bool bLinear)
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/calch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/editconf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_param(InteractionsOfType*, int, int, gmx::ArrayRef<const double>, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:55:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
55 | void add_param(InteractionsOfType* ps, int ai, int aj, gmx::ArrayRef<const real> c, const char* s)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
64 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm, s ? s : ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:64:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite4_atoms(InteractionsOfType*, int, int, int, int, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
101 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:101:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_atoms(InteractionsOfType*, int, int, int, int, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
90 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:90:66: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_cmap_param(InteractionsOfType*, int, int, int, int, int, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
70 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, {}, s ? s : ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:70:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite2_param(InteractionsOfType*, int, int, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
77 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:77:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp: In function 'void add_vsite3_param(InteractionsOfType*, int, int, int, int, real, real)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
84 | ps->interactionTypes.emplace_back(InteractionOfType(atoms, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:84:73: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/add_par.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/fflibutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/convparm.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void enter_function(const InteractionsOfType*, t_functype, int, real, gmx_ffparams_t*, InteractionList*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_maxwell_velocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {std::pair<InteractionOfType, int>}; _Tp = std::pair<InteractionOfType, int>; _Alloc = std::allocator<std::pair<InteractionOfType, int> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<std::pair<InteractionOfType, int> >::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType>, gmx::ArrayRef<const InteractionOfType>, t_atoms*, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
252 | static std::vector<InteractionOfType> clean_dih(gmx::ArrayRef<const InteractionOfType> dih,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:252:39: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<std::pair<InteractionOfType, int>*, std::vector<std::pair<InteractionOfType, int> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genconf.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__final_insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1881 | __final_insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1881:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_6ring(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, real, real, real, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1666 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_his(t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp: In function 'void gen_pad(t_atoms*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<InteractionsOfType>, t_excls*, gmx::ArrayRef<MoleculePatchDatabase>, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
674 | ang.push_back(InteractionOfType(atomNumbers, {}, name));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:674:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:102: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
725 | dih.push_back(InteractionOfType(atomNumbers, {}, name));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:725:102: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:82: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
735 | dih.push_back(InteractionOfType(atoms, {}, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:735:82: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:90: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
754 | pai.push_back(InteractionOfType(atoms, {}, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:754:90: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | ang.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:809:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
847 | dih.push_back(InteractionOfType(atomNumbers, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:847:79: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:47:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1977:31: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1977 | std::__final_insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
889 | rtpFFDB[0].bRemoveDihedralIfWithImproper);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:889:65: note: parameter passing for argument of type 'gmx::ArrayRef<const InteractionOfType>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
389 | improper.emplace_back(InteractionOfType(ai, {}, bondeds.s));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_ad.cpp:389:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_trp(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'int gen_vsites_tyr(PreprocessingAtomTypes*, std::vector<gmx::BasicVector<double> >*, t_atom**, char****, int**, int**, int**, t_symtab*, int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int**, t_atoms*, int**, gmx::ArrayRef<InteractionsOfType>, int, int*, int, gmx::ArrayRef<const VirtualSiteTopology>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genion.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genhydro.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void expand_hackblocks_one(const MoleculePatchDatabase&, std::string, std::vector<MoleculePatch>*, bool, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp: In function 'void do_vsites(gmx::ArrayRef<const PreprocessResidue>, PreprocessingAtomTypes*, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, gmx::ArrayRef<InteractionsOfType>, int**, int**, real, bool, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
637 | add_param(plist, ai, aj, c, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:637:14: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:101: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2247 | *parm = InteractionOfType(newAtomNumber, parm->forceParam(), parm->interactionTypeName());
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gen_vsite.cpp:2247:101: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gmxcpp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_nextnb.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&, char**, const InteractionOfType&, int&, int&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'int PreprocessingAtomTypes::addType(t_symtab*, const t_atom&, const string&, const InteractionOfType&, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/streambuf:41,
from /usr/include/c++/10/bits/streambuf_iterator.h:35,
from /usr/include/c++/10/iterator:66,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const AtomTypeData&}; _Tp = AtomTypeData; _Alloc = std::allocator<AtomTypeData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<AtomTypeData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/arm-linux-gnueabihf/c++/10/bits/c++allocator.h:33,
from /usr/include/c++/10/bits/allocator.h:46,
from /usr/include/c++/10/string:41,
from /usr/include/c++/10/bits/locale_classes.h:40,
from /usr/include/c++/10/bits/ios_base.h:41,
from /usr/include/c++/10/streambuf:41,
from /usr/include/c++/10/bits/streambuf_iterator.h:35,
from /usr/include/c++/10/iterator:66,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/ext/new_allocator.h: In member function 'void PreprocessingAtomTypes::renumberTypes(gmx::ArrayRef<InteractionsOfType>, gmx_mtop_t*, int*, bool)':
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
150 | { ::new((void *)__p) _Up(std::forward<_Args>(__args)...); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/ext/new_allocator.h:150:4: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/gpp_atomtype.cpp:39:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<AtomTypeData*, std::vector<AtomTypeData> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void copyPreprocessResidues(const PreprocessResidue&, PreprocessResidue*, t_symtab*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const MoleculePatch&}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hizzie.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp: In constructor 'InteractionOfType::InteractionOfType(gmx::ArrayRef<const int>, gmx::ArrayRef<const double>, const string&)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/grompp.cpp:111:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
111 | InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/hackblock.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void mergeAtomModifications(const MoleculePatchDatabase&, MoleculePatchDatabase*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.h:38,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/makeexclusiondistances.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<double> makeExclusionDistances(const t_atoms*, AtomProperties*, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp: In function 'int nm2type(int, t_nm2type*, t_symtab*, t_atoms*, PreprocessingAtomTypes*, int*, InteractionsOfType*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
342 | k = atype->addType(tab, atoms->atom[i], type, InteractionOfType({}, {}),
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/nm2type.cpp:342:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In function 'void insert_mols(int, int, int, real, real, t_atoms*, t_symtab*, std::vector<gmx::BasicVector<double> >*, const std::set<int>&, const t_atoms&, gmx::ArrayRef<gmx::BasicVector<double> >, int, real (*)[3], const string&, const real*, RotationType)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:166:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | static void insert_mols(int nmol_insrt,
| ^~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/h_db.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void read_h_db_file(const char*, std::vector<MoleculePatchDatabase>*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp: In member function 'virtual int gmx::{anonymous}::InsertMolecules::run()':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/insert_molecules.cpp:584:16: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
584 | insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_, &atoms, &top_.symtab,
| ~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
585 | &x_, removableAtoms, atomsInserted, xInserted, ePBCForOutput, box_, positionFile_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | deltaR_, enumRot_);
| ~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pgutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_atom&}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp: In function 'pull_t* set_pull_init(t_inputrec*, const gmx_mtop_t*, real (*)[3], real (*)[3], real, warninp_t)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:553:53: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
553 | bool groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
554 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | pbc, g, c_pullGroupSmallGroupThreshold);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readpull.cpp:584:52: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
584 | groupObeysPbc = pullCheckPbcWithinGroup(
| ~~~~~~~~~~~~~~~~~~~~~~~^
585 | *pull_work, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(x), mtop->natoms),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | pbc, g, c_pullGroupPbcMargin);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/readrot.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void add_atom_to_restp(PreprocessResidue*, t_symtab*, int, const MoleculePatch*)':
/usr/include/c++/10/bits/vector.tcc:161:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
161 | _M_realloc_insert(begin() + (__position - cbegin()), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, t_atoms*, t_symtab*, gmx::ArrayRef<gmx::BasicVector<double> >, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:1305:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1305 | void match_atomnames_with_rtp(gmx::ArrayRef<PreprocessResidue> usedPpResidues,
| ^~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'void sort_pdbatoms(gmx::ArrayRef<const PreprocessResidue>, int, t_atoms**, t_atoms**, std::vector<gmx::BasicVector<double> >*, t_blocka*, char***)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual int gmx::{anonymous}::pdb2gmx::run()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:2149:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2149 | match_atomnames_with_rtp(restp_chain, hb_chain, pdba, &symtab, x, bVerbose_);
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2gmx.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__unguarded_linear_insert(_RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Val_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1819:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1819 | __unguarded_linear_insert(_RandomAccessIterator __last,
| ^~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__insertion_sort(_RandomAccessIterator, _RandomAccessIterator, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1839 | __insertion_sort(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1839:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__adjust_heap(_RandomAccessIterator, _Distance, _Distance, _Tp, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Distance = int; _Tp = InteractionOfType; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:223:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
223 | __adjust_heap(_RandomAccessIterator __first, _Distance __holeIndex,
| ^~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__make_heap(_RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
339 | __make_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:339:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h: In function 'void std::__pop_heap(_RandomAccessIterator, _RandomAccessIterator, _RandomAccessIterator, _Compare&) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
253 | __pop_heap(_RandomAccessIterator __first, _RandomAccessIterator __last,
| ^~~~~~~~~~
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_heap.h:253:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h: In function 'void std::__introsort_loop(_RandomAccessIterator, _RandomAccessIterator, _Size, _Compare) [with _RandomAccessIterator = __gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >; _Size = int; _Compare = __gnu_cxx::__ops::_Iter_comp_iter<bool (*)(const InteractionOfType&, const InteractionOfType&)>]':
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1945 | __introsort_loop(_RandomAccessIterator __first,
| ^~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1945:5: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
In file included from /usr/include/c++/10/bits/stl_algo.h:61,
from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_heap.h:424:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
424 | std::__pop_heap(__first, __last, __last, __comp);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h:1959:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1959 | std::__introsort_loop(__cut, __last, __depth_limit, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1666:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1666 | std::__make_heap(__first, __middle, __comp);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp: In function 'void pdb2top(FILE*, const char*, const char*, t_atoms*, std::vector<gmx::BasicVector<double> >*, PreprocessingAtomTypes*, t_symtab*, gmx::ArrayRef<const PreprocessResidue>, gmx::ArrayRef<PreprocessResidue>, gmx::ArrayRef<MoleculePatchDatabase>, bool, bool, bool, const char*, real, gmx::ArrayRef<const DisulfideBond>, real, real, bool, bool, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
782 | add_param(psb, ai, aj, {}, patch.s.c_str());
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:782:26: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
796 | add_param(psb, i, i + 1, {}, nullptr); /* C-O */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:796:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
797 | add_param(psb, i, i + 2, {}, nullptr); /* C-OA */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:797:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
798 | add_param(psb, i + 2, i + 3, {}, nullptr); /* OA-H */
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:798:38: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
803 | add_param(psb, i, i + k + 1, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:803:42: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
729 | add_param(ps, ai, aj, {}, nullptr);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:729:18: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/algorithm:62,
from /<<PKGBUILDDIR>>/src/gromacs/math/vectypes.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/pdb2top.cpp:39:
/usr/include/c++/10/bits/stl_algo.h:1974:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1974 | std::__introsort_loop(__first, __last,
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
1975 | std::__lg(__last - __first) * 2,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1976 | __comp);
| ~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1886:25: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1886 | std::__insertion_sort(__first, __first + int(_S_threshold), __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_algo.h:1891:23: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1891 | std::__insertion_sort(__first, __last, __comp);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In function 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
721 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:721:7: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp: In function 'PreprocessingAtomTypes read_atype(const char*, t_symtab*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
93 | at.addType(tab, *a, name, InteractionOfType({}, {}), 0, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:93:67: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/resall.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/solvate.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_solvate(int, char**)':
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
1665 | _M_range_insert(__pos, __first, __last,
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
1666 | std::__iterator_category(__first));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1665:19: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const SpecialBond&}; _Tp = SpecialBond; _Alloc = std::allocator<SpecialBond>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<SpecialBond>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/specbond.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<SpecialBond> generateSpecialBonds()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<SpecialBond*, std::vector<SpecialBond> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void readResidueDatabase(const string&, std::vector<PreprocessResidue>*, PreprocessingAtomTypes*, t_symtab*, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp: In function 'void convert_harmonics(gmx::ArrayRef<MoleculeInformation>, PreprocessingAtomTypes*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
231 | InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:231:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tomorse.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/ter_db.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {MoleculePatch}; _Tp = MoleculePatch; _Alloc = std::allocator<MoleculePatch>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<MoleculePatch>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = t_atom; _Alloc = std::allocator<t_atom>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_atom>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void read_ter_db_file(const char*, std::vector<MoleculePatchDatabase>*, PreprocessingAtomTypes*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<MoleculePatch*, std::vector<MoleculePatch> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_atom*, std::vector<t_atom> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp: In function 'void make_shake(gmx::ArrayRef<InteractionsOfType>, t_atoms*, int)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | InteractionOfType(atomNumbers, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:162:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
194 | add_param_to_list(&(plist[F_CONSTR]), InteractionOfType(atomNumbers, forceParm));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:194:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topshake.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp: In function 'char** read_topol(const char*, const char*, const char*, const char*, t_symtab*, PreprocessingAtomTypes*, std::vector<MoleculeInformation>*, std::unique_ptr<MoleculeInformation>*, gmx::ArrayRef<InteractionsOfType>, int*, double*, t_gromppopts*, real*, std::vector<gmx_molblock_t>*, bool*, bool, bool, bool, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
135 | pairs->interactionTypes.emplace_back(InteractionOfType(atomNumbers, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:135:87: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/topio.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp: In function 'void print_bondeds(FILE*, int, Directive, int, int, gmx::ArrayRef<const InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
340 | atype.addType(&stab, *a, buf, InteractionOfType({}, {}), 0, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:340:63: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_LJCpairsNB(MoleculeInformation*, int, InteractionsOfType*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:106: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2658 | add_param_to_list(&mol->interactions[F_LJC_PAIRS_NB], InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2658:106: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toputil.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void add_param_to_list(InteractionsOfType*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_at(t_symtab*, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, int, t_nbparam***, t_nbparam***, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
541 | InteractionOfType interactionType({}, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:541:57: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_vsitesn(Directive, gmx::ArrayRef<InteractionsOfType>, t_atoms*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2443 | add_param_to_list(&bond[ftype], InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2443:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'int add_atomtype_decoupled(t_symtab*, PreprocessingAtomTypes*, t_nbparam***, t_nbparam***)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2574 | nr = at->addType(symtab, atom, "decoupled", InteractionOfType({}, forceParam, ""), -1, 0);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2574:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'bool calc_vsite3_param(PreprocessingAtomTypes*, InteractionOfType*, t_atoms*, gmx::ArrayRef<const VsiteBondedInteraction>, gmx::ArrayRef<const VsiteBondedInteraction>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:402:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
402 | static bool calc_vsite3_param(PreprocessingAtomTypes* atypes,
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:402:13: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bond(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, bool, bool, real, bool, bool*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1984 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1984:50: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VsiteBondedInteraction}; _Tp = VsiteBondedInteraction; _Alloc = std::allocator<VsiteBondedInteraction>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VsiteBondedInteraction>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void enter_bonded(int, std::vector<VsiteBondedInteraction>*, const InteractionOfType&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VsiteBondedInteraction*, std::vector<VsiteBondedInteraction> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_cmap(Directive, gmx::ArrayRef<InteractionsOfType>, gmx::ArrayRef<InteractionsOfType>, t_atoms*, PreprocessingAtomTypes*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2336 | InteractionOfType param(atoms, forceParam, "");
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2336:64: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'void lo_set_force_const(InteractionsOfType*, real*, int, bool, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp: In function 'int set_vsites(bool, t_atoms*, PreprocessingAtomTypes*, gmx::ArrayRef<InteractionsOfType>)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
821 | bERROR = calc_vsite3_param(atypes, ¶m, atoms, allVsiteBondeds.bonds,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
822 | allVsiteBondeds.angles);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:821:55: note: parameter passing for argument of type 'gmx::ArrayRef<const VsiteBondedInteraction>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void generate_nbparams(int, int, InteractionsOfType*, PreprocessingAtomTypes*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:103:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
127 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:127:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
151 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:151:105: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:97: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
184 | interactions->interactionTypes.emplace_back(InteractionOfType({}, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:184:97: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp: In function 'int gmx_x2top(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
137 | add_param_to_list(bond, InteractionOfType(atoms, forceParam));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:137:76: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | param = InteractionOfType(param.atoms(), forceParam);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/x2top.cpp:239:60: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bondtype(InteractionsOfType*, const InteractionOfType&, int, int, bool, const char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
711 | InteractionOfType(b.atoms(), b.forceParam(), b.interactionTypeName()));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:711:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
730 | bt->interactionTypes.emplace_back(InteractionOfType(atoms, forceParam, b.interactionTypeName()));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:730:103: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_bt(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
851 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:851:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/xlate.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp: In function 'void push_dihedraltype(Directive, gmx::ArrayRef<InteractionsOfType>, PreprocessingBondAtomType*, char*, warninp*)':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1019 | push_bondtype(&(bt[ftype]), InteractionOfType(atoms, forceParam), 4, ftype, bAllowRepeat, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1019:68: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'void push_cmaptype(Directive, gmx::ArrayRef<InteractionsOfType>, int, PreprocessingAtomTypes*, PreprocessingBondAtomType*, char*, warninp*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1286 | push_bondtype(&(bt[ftype]), InteractionOfType(atomTypes, forceParam), nral, ftype, FALSE, line, wi);
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:1286:72: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void convert_pairs_to_pairsQ(gmx::ArrayRef<InteractionsOfType>, real, t_atoms*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
2606 | paramnew.emplace_back(InteractionOfType(param.atoms(), forceParam, ""));
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:2606:78: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/toppush.cpp:39:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/crosscorr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {InteractionOfType&}; _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::_M_erase(std::vector<_Tp, _Alloc>::iterator) [with _Tp = InteractionOfType; _Alloc = std::allocator<InteractionOfType>]':
/usr/include/c++/10/bits/vector.tcc:171:5: note: parameter passing for argument of type 'std::vector<InteractionOfType>::iterator' changed in GCC 7.1
171 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/expfit.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_four_core(int, real*, real*, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/gmx_lmcurve.cpp
/usr/include/c++/10/bits/stl_vector.h: In function 'void low_do_autocorr(const char*, const gmx_output_env_t*, const char*, int, int, int, real**, real, long unsigned int, int, gmx_bool, gmx_bool, gmx_bool, real, real, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void clean_vsite_bondeds(gmx::ArrayRef<InteractionsOfType>, int, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/vsite_parm.cpp:39:
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1431:24: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<InteractionOfType*, std::vector<InteractionOfType> >' changed in GCC 7.1
1431 | { return _M_erase(begin() + (__position - cbegin())); }
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/integrate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/polynomials.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/statistics/statistics.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/abstractdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/analysisdata.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/manyautocorrelation.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z16many_auto_correlPSt6vectorIS_IdSaIdEESaIS1_EE._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int many_auto_correl(std::vector<std::vector<double> >*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datamodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataproxy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/arraydata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::AbstractAnalysisArrayData::AbstractAnalysisArrayData()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/frameaverager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/lifetime.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/dataframe.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/displacement.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::AnalysisDataDisplacementModule::frameFinished(const gmx::AnalysisDataFrameHeader&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/modules/plot.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::AnalysisDataValue&}; _Tp = gmx::AnalysisDataValue; _Alloc = std::allocator<gmx::AnalysisDataValue>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::AnalysisDataValue>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::internal::AnalysisDataStorageFrameData::addPointSet(int, int, gmx::ArrayRef<const gmx::AnalysisDataValue>)':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:583:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
583 | void AnalysisDataStorageFrameData::addPointSet(int dataSetIndex,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:44:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::AnalysisDataValue*, std::vector<gmx::AnalysisDataValue> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp: In member function 'void gmx::AnalysisDataStorageFrame::finishPointSet()':
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
714 | data_->addPointSet(currentDataSet_, firstColumn,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
715 | makeConstArrayRef(values_).subArray(begin, end - begin));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/analysisdata/datastorage.cpp:714:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::AnalysisDataValue>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/coordinatefile.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/outputselector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setforces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setprecision.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/outputadapters/setvelocities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysissettings.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/pairdist.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::FreeVolume::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/freevolume.cpp:44:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/analysismodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/sasa.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::analysismodules::{anonymous}::Sasa::initAnalysis(const gmx::TrajectoryAnalysisSettings&, const gmx::TopologyInformation&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/runnercommon.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/check.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/check.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/convert_tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/eneconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/make_ndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/mk_angndx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/pme_error.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjcat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tune_pme.cpp
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp: In function 'int gmx_trjconv(int, char**)':
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1245 | put_atoms_in_compact_unitcell(ePBC, ecenter, fr.box, positionsArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tools/trjconv.cpp:1245:66: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/10/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:400:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
400 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
708 | lincs_update_atoms(lincsd, th, 1.0, sol, r,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
709 | (econq != ConstraintVariable::Force) ? invmass : nullptr, fp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1079:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1079 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1141:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1141 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1590 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1601:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1601 | stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1602 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1613:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1613 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1634:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1634 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1771:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1771 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1790:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1790 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
56 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:143:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
144 | state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::Update*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1752:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1752 | upd->deform()->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1868:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1868 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1896 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->sd()->randomize_group, upd->sd()->boltzfac);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function 'gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:338:26: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
338 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
741 | void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, int, double, const gmx::DensityFittingForceProviderState&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:79:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
79 | scaleToLattice({ &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:166:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
167 | { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:171:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:172:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
172 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:210:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
210 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:258:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
258 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:551:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:896:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
896 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1035:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1035 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1036 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
952 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:711:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
728 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
730 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
731 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
732 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
733 | &dvdlambda_lj, pmeFlags);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1004 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1384 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1393 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:845:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
845 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
846 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
847 | ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ems->s.lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
848 | graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:905:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
905 | sum_dhdl(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:379:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
379 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:421:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
421 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
422 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
424 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:437:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
437 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
438 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
439 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:451:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
451 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
452 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
453 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:509:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
509 | dd_collect_vec(cr->dd, state, flocal, ftemp);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:519:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
519 | mimicCommunicator.sendForces(ftemp, state_global->natoms);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:533:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
533 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:749:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
749 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:753:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
753 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
754 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
755 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:767:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
767 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:810:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:815:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
815 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:918:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
918 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
919 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
920 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
921 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
922 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:945:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
945 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
946 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
947 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
948 | fr, runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
949 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1100:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1100 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1128:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1128 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1136:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1136 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1152:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1152 | stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1159:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1159 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1161 | checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1162 | mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1194:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1194 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1266:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1266 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1267:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1267 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1273:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1273 | stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1290:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1290 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1393:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1393 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1429:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1429 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1437:58: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1437 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1455:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1455 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, PaddedHostVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:385:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
385 | initialize_lambdas(fplog, *ir, MASTER(cr), &(state_global->fep_state), state_global->lambda, nullptr);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1858:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1858 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1859 | static_cast<real>(step), &ems.s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1860 | observablesHistory, ems.f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
302 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:551:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
551 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
556 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:567:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
567 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
568 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:581:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
581 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
582 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:641:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
641 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2766:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2766 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2767 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2768 | fcd, state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2769 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2770 | state_work.s.lambda, &state_work.s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2771 | state_work.f.arrayRefWithPadding(), vir, mdatoms, nrnb,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2772 | wcycle, graph, shellfc, fr, runScheduleWork, t, mu_tot,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2773 | vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, const gmx_vsite_t*, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:936:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
936 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1094:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1094 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1095 | nrnb, wcycle, top, box, x, hist, forceWithPadding[Min], force_vir, md, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1096 | lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1097 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1188:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1188 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1189 | wcycle, top, box, posWithPadding[Try], hist, forceWithPadding[Try], force_vir, md,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1190 | enerd, fcd, lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1191 | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::LegacySimulator::do_tpi()':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:591:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
591 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:663:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
663 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
664 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
722 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:745:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
745 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
746 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
747 | &state_global->hist, f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
748 | state_global->lambda, nullptr, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
749 | GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
750 | DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'int gmx::Mdrunner::mdrunner()':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:1395:38: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1395 | constructVsitesGlobal(mtop, globalState->x);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:132:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
132 | void StatePropagatorDataGpu::copyCoordinatesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:147:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
147 | void StatePropagatorDataGpu::copyCoordinatesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_x */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:164:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
164 | void StatePropagatorDataGpu::copyVelocitiesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:180:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
180 | void StatePropagatorDataGpu::copyVelocitiesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_v */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesToGpu(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:204:6: note: parameter passing for argument of type 'const gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
204 | void StatePropagatorDataGpu::copyForcesToGpu(const gmx::ArrayRef<const gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp: In member function 'void gmx::StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::BasicVector<double> >, gmx::AtomLocality)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
229 | void StatePropagatorDataGpu::copyForcesFromGpu(gmx::ArrayRef<gmx::RVec> /* h_f */,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintpotential.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const int&}; _Tp = gmx::Site; _Alloc = std::allocator<gmx::Site>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::Site>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::RestraintForceProvider::RestraintForceProvider(std::shared_ptr<gmx::IRestraintPotential>, const std::vector<int>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::Site*, std::vector<gmx::Site> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:271:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
271 | void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
| ^~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 'void writeXpmAxis(FILE*, const char*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:809:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
809 | static void writeXpmAxis(FILE* out, const char* axis, ArrayRef<const real> label)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx_tng_add_mtop(gmx_tng_trajectory_t, const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<t_matrix> read_xpm_matrix(const char*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::internal::{anonymous}::computeMassesAndCharges(const gmx_mtop_t*, const gmx_ana_pos_t&, std::vector<double>*, std::vector<double>*)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::internal::SelectionData::initializeMassesAndCharges(const gmx_mtop_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -Dlibgromacs_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/basic-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgromacs_d.so.5 -o ../../lib/libgromacs_d.so.5.0.0 CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o CMakeFiles/libgromacs.dir/utility/futil.cpp.o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o CMakeFiles/libgromacs.dir/utility/init.cpp.o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o CMakeFiles/libgromacs.dir/utility/logger.cpp.o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o CMakeFiles/libgromacs.dir/utility/path.cpp.o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o CMakeFiles/libgromacs.dir/math/functions.cpp.o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o CMakeFiles/libgromacs.dir/math/units.cpp.o CMakeFiles/libgromacs.dir/math/utilities.cpp.o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o CMakeFiles/libgromacs.dir/random/seed.cpp.o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o CMakeFiles/libgromacs.dir/topology/block.cpp.o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o CMakeFiles/libgromacs.dir/topology/idef.cpp.o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o CMakeFiles/libgromacs.dir/topology/index.cpp.o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o CMakeFiles/libgromacs.dir/topology/topology.cpp.o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o CMakeFiles/libgromacs.dir/pulling/output.cpp.o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o CMakeFiles/libgromacs.dir/awh/awh.cpp.o CMakeFiles/libgromacs.dir/awh/bias.cpp.o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o CMakeFiles/libgromacs.dir/awh/grid.cpp.o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o CMakeFiles/libgromacs.dir/simd/support.cpp.o CMakeFiles/libgromacs.dir/imd/imd.cpp.o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o CMakeFiles/libgromacs.dir/gmxana/anadih.cpp.o CMakeFiles/libgromacs.dir/gmxana/angle_correction.cpp.o CMakeFiles/libgromacs.dir/gmxana/binsearch.cpp.o CMakeFiles/libgromacs.dir/gmxana/cmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/dens_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/dlist.cpp.o CMakeFiles/libgromacs.dir/gmxana/eigio.cpp.o CMakeFiles/libgromacs.dir/gmxana/fitahx.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_anaeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_analyze.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_angle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_awh.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_bundle.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_chi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_cluster.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_clustsize.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_confrms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_covar.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_current.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_density.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densmap.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_densorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dielectric.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dipoles.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_disre.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_do_dssp.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dos.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_dyecoupl.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_enemat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_energy.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_filter.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_gyrate.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_h2order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hbond.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helix.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_helixorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_hydorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_lie.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_make_edi.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mdmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_mindist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_msd.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmeig.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmens.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_nmtraj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_order.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_polystat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_potential.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_principal.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rama.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rms.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsdist.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rmsf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotacf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_rotmat.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saltbr.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sans.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_saxs.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sigeps.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_sorient.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spatial.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_spol.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_tcaf.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_traj.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_trjorder.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_vanhove.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_velacc.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wham.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_wheel.cpp.o CMakeFiles/libgromacs.dir/gmxana/gmx_xpm2ps.cpp.o CMakeFiles/libgromacs.dir/gmxana/hxprops.cpp.o CMakeFiles/libgromacs.dir/gmxana/nrama.cpp.o CMakeFiles/libgromacs.dir/gmxana/nsfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/powerspect.cpp.o CMakeFiles/libgromacs.dir/gmxana/pp2shift.cpp.o CMakeFiles/libgromacs.dir/gmxana/princ.cpp.o CMakeFiles/libgromacs.dir/gmxana/sfactor.cpp.o CMakeFiles/libgromacs.dir/gmxana/thermochemistry.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/add_par.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/calch.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/convparm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/editconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/fflibutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_ad.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_maxwell_velocities.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gen_vsite.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genconf.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genhydro.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genion.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/genrestr.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gmxcpp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_bond_atomtype.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/gpp_nextnb.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/grompp.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/h_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hackblock.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/hizzie.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/insert_molecules.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/makeexclusiondistances.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/nm2type.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2gmx.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pdb2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/pgutil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readir.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readpull.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/readrot.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/resall.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/solvate.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/specbond.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/ter_db.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/tomorse.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topdirs.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topio.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toppush.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/topshake.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/toputil.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/vsite_parm.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/x2top.cpp.o CMakeFiles/libgromacs.dir/gmxpreprocess/xlate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/autocorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/crosscorr.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/expfit.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/gmx_lmcurve.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/integrate.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/manyautocorrelation.cpp.o CMakeFiles/libgromacs.dir/correlationfunctions/polynomials.cpp.o CMakeFiles/libgromacs.dir/statistics/statistics.cpp.o CMakeFiles/libgromacs.dir/analysisdata/abstractdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/analysisdata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/arraydata.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataframe.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodule.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datamodulemanager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/dataproxy.cpp.o CMakeFiles/libgromacs.dir/analysisdata/datastorage.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/average.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/displacement.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/frameaverager.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/histogram.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/lifetime.cpp.o CMakeFiles/libgromacs.dir/analysisdata/modules/plot.cpp.o CMakeFiles/libgromacs.dir/coordinateio/coordinatefile.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadaptercontainer.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/outputselector.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setatoms.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setforces.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setprecision.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setstarttime.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/settimestep.cpp.o CMakeFiles/libgromacs.dir/coordinateio/outputadapters/setvelocities.cpp.o CMakeFiles/libgromacs.dir/coordinateio/requirements.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysismodule.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/analysissettings.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/cmdlinerunner.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/angle.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/convert_trj.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/distance.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/extract_cluster.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/freevolume.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/pairdist.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/rdf.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/sasa.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/select.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/surfacearea.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/modules/trajectory.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/runnercommon.cpp.o CMakeFiles/libgromacs.dir/trajectoryanalysis/topologyinformation.cpp.o CMakeFiles/libgromacs.dir/tools/check.cpp.o CMakeFiles/libgromacs.dir/tools/convert_tpr.cpp.o CMakeFiles/libgromacs.dir/tools/dump.cpp.o CMakeFiles/libgromacs.dir/tools/eneconv.cpp.o CMakeFiles/libgromacs.dir/tools/make_ndx.cpp.o CMakeFiles/libgromacs.dir/tools/mk_angndx.cpp.o CMakeFiles/libgromacs.dir/tools/pme_error.cpp.o CMakeFiles/libgromacs.dir/tools/report_methods.cpp.o CMakeFiles/libgromacs.dir/tools/trjcat.cpp.o CMakeFiles/libgromacs.dir/tools/trjconv.cpp.o CMakeFiles/libgromacs.dir/tools/tune_pme.cpp.o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o CMakeFiles/libgromacs.dir/fft/fft.cpp.o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o CMakeFiles/libgromacs.dir/options/options.cpp.o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o CMakeFiles/libgromacs.dir/selection/params.cpp.o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o CMakeFiles/libgromacs.dir/selection/position.cpp.o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o CMakeFiles/libgromacs.dir/selection/selection.cpp.o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/energyelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/alltoall.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_protocol.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/barrier.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_send_recv.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/bcast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/p2p_wait.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/collective.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/profile.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/comm.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/event.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/reduce_fast.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/gather.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scatter.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/group.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_init.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/topology.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/list.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/type.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/scan.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/numa_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/once.cpp.o fileio/CMakeFiles/vmddlopen.dir/__/__/external/vmd_molfile/vmddlopen.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o /usr/lib/arm-linux-gnueabihf/libhwloc.so -ldl -lrt /usr/lib/arm-linux-gnueabihf/libfftw3.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so -lpthread -lm /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs && /usr/bin/cmake -E cmake_symlink_library ../../lib/libgromacs_d.so.5.0.0 ../../lib/libgromacs_d.so.5 ../../lib/libgromacs_d.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target libgromacs
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/depend
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/gmx.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
Scanning dependencies of target gmx
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/gmx.dir/build.make src/programs/CMakeFiles/gmx.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/gmx.cpp.o -c /<<PKGBUILDDIR>>/src/programs/gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmx.dir/legacymodules.cpp.o -c /<<PKGBUILDDIR>>/src/programs/legacymodules.cpp
Scanning dependencies of target gmxapi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/context.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/context.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/gmxapi.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/gmxapi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/md.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/md.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/mdsignals.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/mdsignals.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmx.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmx.dir/gmx.cpp.o CMakeFiles/gmx.dir/legacymodules.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o CMakeFiles/view_objlib.dir/view/3dview.cpp.o CMakeFiles/view_objlib.dir/view/buttons.cpp.o CMakeFiles/view_objlib.dir/view/dialogs.cpp.o CMakeFiles/view_objlib.dir/view/fgrid.cpp.o CMakeFiles/view_objlib.dir/view/filter.cpp.o CMakeFiles/view_objlib.dir/view/logo.cpp.o CMakeFiles/view_objlib.dir/view/manager.cpp.o CMakeFiles/view_objlib.dir/view/molps.cpp.o CMakeFiles/view_objlib.dir/view/nleg.cpp.o CMakeFiles/view_objlib.dir/view/nmol.cpp.o CMakeFiles/view_objlib.dir/view/popup.cpp.o CMakeFiles/view_objlib.dir/view/pulldown.cpp.o CMakeFiles/view_objlib.dir/view/view.cpp.o CMakeFiles/view_objlib.dir/view/x11.cpp.o CMakeFiles/view_objlib.dir/view/xdlg.cpp.o CMakeFiles/view_objlib.dir/view/xdlghi.cpp.o CMakeFiles/view_objlib.dir/view/xdlgitem.cpp.o CMakeFiles/view_objlib.dir/view/xmb.cpp.o CMakeFiles/view_objlib.dir/view/xutil.cpp.o -o ../../bin/gmx_d ../../lib/libgromacs_d.so.5.0.0 /usr/lib/arm-linux-gnueabihf/libX11.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 98%] Built target gmx
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/session.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/session.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -Dgmxapi_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi.dir/tpr.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tpr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmxapi_d.so.0 -o ../../../lib/libgmxapi_d.so.0.1.0 CMakeFiles/gmxapi.dir/context.cpp.o CMakeFiles/gmxapi.dir/exceptions.cpp.o CMakeFiles/gmxapi.dir/gmxapi.cpp.o CMakeFiles/gmxapi.dir/md.cpp.o CMakeFiles/gmxapi.dir/mdmodule.cpp.o CMakeFiles/gmxapi.dir/mdsignals.cpp.o CMakeFiles/gmxapi.dir/session.cpp.o CMakeFiles/gmxapi.dir/status.cpp.o CMakeFiles/gmxapi.dir/system.cpp.o CMakeFiles/gmxapi.dir/version.cpp.o CMakeFiles/gmxapi.dir/workflow.cpp.o CMakeFiles/gmxapi.dir/tpr.cpp.o ../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp && /usr/bin/cmake -E cmake_symlink_library ../../../lib/libgmxapi_d.so.0.1.0 ../../../lib/libgmxapi_d.so.0 ../../../lib/libgmxapi_d.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target gmxapi
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -j4 -C build/basic tests
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/make -f CMakeFiles/Makefile2 tests
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 97
/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Raspbian-2020.6-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.6-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
[ 1%] Built target scanner
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
[ 2%] Built target tng_io_obj
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
[ 4%] Built target thread_mpi
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
[ 4%] Built target release-version-info
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 4%] Built target lmfit_objlib
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googletest /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color=
[ 4%] Built target vmddlopen
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
[ 4%] Built target linearalgebra
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs /<<PKGBUILDDIR>>/build/basic/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 5%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
[ 5%] Built target mdrun_objlib
Scanning dependencies of target gtest
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googletest/include -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs /<<PKGBUILDDIR>>/build/basic/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 64%] Built target libgromacs
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp /<<PKGBUILDDIR>>/build/basic/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 65%] Built target gmxapi
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 65%] Built target gtest
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
Scanning dependencies of target gmock
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=0 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 65%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils /<<PKGBUILDDIR>>/build/basic/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o
/usr/bin/ranlib ../../lib/libtestutils.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 68%] Built target testutils
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils/tests /<<PKGBUILDDIR>>/build/basic/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/testutils/tests /<<PKGBUILDDIR>>/build/basic/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build
Scanning dependencies of target utility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
Scanning dependencies of target testutils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
Scanning dependencies of target mdrun_test_infrastructure
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 68%] Built target utility-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
[ 68%] Built target testutils-mpi-test
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
Scanning dependencies of target utility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdlib-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target mdrun_test_infrastructure
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target onlinehelp-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 69%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 70%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target mdlib-test
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 71%] Built target fft-test
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 72%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target ewald-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target mdrunutility-test-shared
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 73%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 74%] Built target utility-test
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 75%] Built target onlinehelp-test
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target mdspan-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 76%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 77%] Built target random-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 78%] Built target options-test
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target math-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target taskassignment-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 80%] Built target table-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const float&, double, const float&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 80%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target gmxana-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target compat-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 81%] Built target pdb2gmx2-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 82%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=0 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 84%] Built target pdb2gmx1-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 85%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target gmxpreprocess-test
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 86%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 87%] Built target tool-test
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 88%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-modules-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target mdrun-modules-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-io-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 89%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/dispersion_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-output-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 90%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target mdrun-io-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 91%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 92%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target mdrun-non-integrator-test
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 93%] Built target gmxapi-mpi-test
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 94%] Built target gmxapi-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 95%] Built target workflow-details-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 96%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[ 97%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
cd /<<PKGBUILDDIR>>/build/basic && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic /<<PKGBUILDDIR>>/build/basic/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic'
(cd build/basic; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic/lib ctest -V || dpkg-architecture -i hurd-i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (3 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (4 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (2 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (23 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (15 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (2 ms)
1: [----------] 34 tests from ReferenceDataTest (56 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (0 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (2 ms)
1: [----------] 4 tests from XvgTests (8 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (89 ms total)
1: [ PASSED ] 59 tests.
1/54 Test #1: TestUtilsUnitTests .................. Passed 2.71 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (1 ms)
2: [----------] 1 test from MpiSelfTest (1 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (1 ms total)
2: [ PASSED ] 1 test.
2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.15 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 347 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<float, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (2 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (1 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 4 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (1 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (53 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (2 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (57 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (2 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (2 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
3: [----------] 6 tests from TreeValueTransformTest (6 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (0 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (0 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (1 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (2 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (1 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (5 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
3: [----------] 7 tests from LoggerTest (11 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (0 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (1 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (2 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (16 ms)
3: [----------] 2 tests from PathTest (17 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (1 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (2 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (1 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (0 ms)
3: [----------] 6 tests from ReplaceAllTest (0 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
3: [----------] 10 tests from TextLineWrapperTest (4 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (1 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (1 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (0 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (1 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
3: [----------] 6 tests from TextWriterTest (3 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (0 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (1 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (2 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 347 tests from 56 test cases ran. (130 ms total)
3: [ PASSED ] 347 tests.
3/54 Test #3: UtilityUnitTests .................... Passed 0.25 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (2 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (4 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (5 ms total)
4: [ PASSED ] 2 tests.
4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.14 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 187 tests from 13 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (0 ms)
5: [----------] 1 test from VerletBufferConstraintTest (2 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (23 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (2 ms)
5: [----------] 2 tests from PrEbinTest (25 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (1 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (1 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (1 ms)
5: [----------] 4 tests from ShakeTest (4 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (5 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (1 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (1 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (1 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (1 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (1 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (1 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (1 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (0 ms)
5: [----------] 9 tests from UpdateGroups (7 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (25 ms)
5: [----------] 1 test from UpdateGroupsCog (26 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (2 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (35 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (16 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (14 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (15 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (4 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as single precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (69 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (14 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (14 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as single precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (14 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (222 ms total)
5:
5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (1 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (1 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (3 ms total)
5:
5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (1 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (3 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (34 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (13 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (12 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (13 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (20 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (13 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (160 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (5 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (8 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (5 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (5 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (9 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (9 ms)
5: [----------] 13 tests from WithParameters/SettleTest (63 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 187 tests from 13 test cases ran. (558 ms total)
5: [ PASSED ] 187 tests.
5/54 Test #5: MdlibUnitTest ....................... Passed 0.66 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (2 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (30 ms)
6: [----------] 2 tests from DensityFittingTest (33 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (2 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (1 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (0 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (5 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (1 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (0 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (0 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (0 ms)
6: [----------] 3 tests from ElectricFieldTest (1 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (40 ms total)
6: [ PASSED ] 20 tests.
6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.10 sec
test 7
Start 7: CommandLineUnitTests
7: Test command: /<<PKGBUILDDIR>>/build/basic/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CommandLineUnitTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 59 tests from 7 test cases.
7: [----------] Global test environment set-up.
7: [----------] 3 tests from CommandLineHelpModuleTest
7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (18 ms)
7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (2 ms)
7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (18 ms)
7: [----------] 3 tests from CommandLineHelpModuleTest (38 ms total)
7:
7: [----------] 7 tests from CommandLineHelpWriterTest
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (3 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (2 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (2 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
7: [----------] 7 tests from CommandLineHelpWriterTest (11 ms total)
7:
7: [----------] 6 tests from CommandLineModuleManagerTest
7: [ RUN ] CommandLineModuleManagerTest.RunsModule
7: [ OK ] CommandLineModuleManagerTest.RunsModule (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (0 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (1 ms)
7: [----------] 6 tests from CommandLineModuleManagerTest (6 ms total)
7:
7: [----------] 13 tests from CommandLineParserTest
7: [ RUN ] CommandLineParserTest.HandlesSingleValues
7: [ OK ] CommandLineParserTest.HandlesSingleValues (1 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (1 ms)
7: [ RUN ] CommandLineParserTest.HandlesString
7: [ OK ] CommandLineParserTest.HandlesString (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (0 ms)
7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (1 ms)
7: [----------] 13 tests from CommandLineParserTest (6 ms total)
7:
7: [----------] 6 tests from CommandLineProgramContextTest
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (1 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (1 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (1 ms)
7: [----------] 6 tests from CommandLineProgramContextTest (3 ms total)
7:
7: [----------] 3 tests from OutputNamesTest
7: [ RUN ] OutputNamesTest.CanBeSuffixed
7: [ OK ] OutputNamesTest.CanBeSuffixed (0 ms)
7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (1 ms)
7: [----------] 3 tests from OutputNamesTest (1 ms total)
7:
7: [----------] 21 tests from ParseCommonArgsTest
7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (1 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (4 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (1 ms)
7: [----------] 21 tests from ParseCommonArgsTest (19 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 59 tests from 7 test cases ran. (84 ms total)
7: [ PASSED ] 59 tests.
7/54 Test #7: CommandLineUnitTests ................ Passed 0.15 sec
test 8
Start 8: DomDecTests
8: Test command: /<<PKGBUILDDIR>>/build/basic/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/DomDecTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 9 tests from 2 test cases.
8: [----------] Global test environment set-up.
8: [----------] 7 tests from HashedMap
8: [ RUN ] HashedMap.InsertsFinds
8: [ OK ] HashedMap.InsertsFinds (0 ms)
8: [ RUN ] HashedMap.NegativeKeysWork
8: [ OK ] HashedMap.NegativeKeysWork (0 ms)
8: [ RUN ] HashedMap.InsertsErases
8: [ OK ] HashedMap.InsertsErases (0 ms)
8: [ RUN ] HashedMap.InsertsOrAssigns
8: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
8: [ RUN ] HashedMap.Clears
8: [ OK ] HashedMap.Clears (0 ms)
8: [ RUN ] HashedMap.LinkedEntries
8: [ OK ] HashedMap.LinkedEntries (0 ms)
8: [ RUN ] HashedMap.ResizesTable
8: [ OK ] HashedMap.ResizesTable (0 ms)
8: [----------] 7 tests from HashedMap (0 ms total)
8:
8: [----------] 2 tests from LocalAtomSetManager
8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (1 ms)
8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
8: [----------] 2 tests from LocalAtomSetManager (1 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 9 tests from 2 test cases ran. (2 ms total)
8: [ PASSED ] 9 tests.
8/54 Test #8: DomDecTests ......................... Passed 0.06 sec
test 9
Start 9: EwaldUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EwaldUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 257 tests from 10 test cases.
9: [----------] Global test environment set-up.
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (2 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (1 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (13 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms)
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (17 ms total)
9:
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (65 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (33 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (10 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (39 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (20 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (21 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (11 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (10 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (11 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (10 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (10 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (10 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (65 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (11 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (11 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (12 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (13 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (12 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (13 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (12 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (12 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (12 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (13 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (12 ms)
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (480 ms total)
9:
9: [----------] 144 tests from SaneInput/PmeGatherTest
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (4 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (15 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (16 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (12 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (11 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (3 ms)
9: [----------] 144 tests from SaneInput/PmeGatherTest (379 ms total)
9:
9: [----------] 16 tests from SaneInput/PmeSolveTest
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (8 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (9 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (6 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (8 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (10 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (7 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (7 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (6 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (12 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (68 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (9 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (6 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (6 ms)
9: [----------] 16 tests from SaneInput/PmeSolveTest (176 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (5 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (4 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (3 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (6 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (4 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (4 ms)
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (37 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (9 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (9 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (6 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (6 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (9 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (9 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (6 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (6 ms)
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (61 ms total)
9:
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (8 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (5 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (9 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (5 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (9 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (5 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (10 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (5 ms)
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (98 ms total)
9:
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (6 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (14 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (7 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (8 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (9 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (10 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (6 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (6 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (7 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (8 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (9 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (10 ms)
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (105 ms total)
9:
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (8 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (18 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (9 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (11 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (13 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (8 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (10 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (18 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (14 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (15 ms)
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (143 ms total)
9:
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (17 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (19 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (25 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (29 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (43 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (41 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (17 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (18 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (24 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (27 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (34 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (38 ms)
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (359 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 257 tests from 10 test cases ran. (2472 ms total)
9: [ PASSED ] 257 tests.
9/54 Test #9: EwaldUnitTests ...................... Passed 2.68 sec
test 10
Start 10: FFTUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FFTUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 14 tests from 4 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from ManyFFTTest
10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (61 ms)
10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (56 ms)
10: [----------] 2 tests from ManyFFTTest (121 ms total)
10:
10: [----------] 1 test from FFTTest
10: [ RUN ] FFTTest.Real2DLength18_15Test
10: [ OK ] FFTTest.Real2DLength18_15Test (20 ms)
10: [----------] 1 test from FFTTest (21 ms total)
10:
10: [----------] 1 test from FFFTest3D
10: [ RUN ] FFFTest3D.Real5_6_9
10: [ OK ] FFFTest3D.Real5_6_9 (11 ms)
10: [----------] 1 test from FFFTest3D (14 ms total)
10:
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (4 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (3 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (6 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (12 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (10 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (3 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (3 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (4 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (31 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (44 ms)
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (121 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 14 tests from 4 test cases ran. (279 ms total)
10: [ PASSED ] 14 tests.
10/54 Test #10: FFTUnitTests ........................ Passed 0.35 sec
test 11
Start 11: GpuUtilsUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GpuUtilsUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 62 tests from 20 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ClfftInitializer
11: [ RUN ] ClfftInitializer.SingleInitializationWorks
11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
11: [ RUN ] ClfftInitializer.TwoInitializationsWork
11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
11: [----------] 2 tests from ClfftInitializer (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/0 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = float
11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/2 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (1 ms)
11: [----------] 2 tests from HostAllocatorTest/3 (1 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/1 (1 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/2 (1 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Swap
11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Comparison
11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/0 (2 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Swap
11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Comparison
11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/1 (1 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Swap
11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Comparison
11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/2 (2 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Swap
11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Comparison
11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/3 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = float
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<float>
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
11:
11: [----------] 1 test from HostAllocatorUntypedTest
11: [ RUN ] HostAllocatorUntypedTest.Comparison
11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<float, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.Move
11: [ OK ] AllocatorTest/0.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/0 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.Move
11: [ OK ] AllocatorTest/1.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/1 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.Move
11: [ OK ] AllocatorTest/2.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/2 (1 ms total)
11:
11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.Move
11: [ OK ] AllocatorTest/3.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/3 (1 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 62 tests from 20 test cases ran. (20 ms total)
11: [ PASSED ] 62 tests.
11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.10 sec
test 12
Start 12: HardwareUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/HardwareUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 4 tests from 1 test case.
12: [----------] Global test environment set-up.
12: [----------] 4 tests from HardwareTopologyTest
12: [ RUN ] HardwareTopologyTest.Execute
12: [ OK ] HardwareTopologyTest.Execute (45 ms)
12: [ RUN ] HardwareTopologyTest.HwlocExecute
12: [ OK ] HardwareTopologyTest.HwlocExecute (49 ms)
12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (41 ms)
12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (32 ms)
12: [----------] 4 tests from HardwareTopologyTest (167 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 4 tests from 1 test case ran. (171 ms total)
12: [ PASSED ] 4 tests.
12/54 Test #12: HardwareUnitTests ................... Passed 0.24 sec
test 13
Start 13: MathUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MathUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 204 tests from 29 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from EmptyArrayRefWithPaddingTest
13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (1 ms)
13: [----------] 1 test from EmptyArrayRefWithPaddingTest (1 ms total)
13:
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (1 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (0 ms total)
13:
13: [----------] 8 tests from TranslateAndScaleTest
13: [ RUN ] TranslateAndScaleTest.identityTransformation
13: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (1 ms)
13: [ RUN ] TranslateAndScaleTest.scalingIdentity
13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
13: [----------] 8 tests from TranslateAndScaleTest (2 ms total)
13:
13: [----------] 12 tests from DensitySimilarityTest
13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (1 ms)
13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (4 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (123 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (134 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (122 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (2 ms)
13: [----------] 12 tests from DensitySimilarityTest (388 ms total)
13:
13: [----------] 6 tests from StructureSimilarityTest
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (1 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
13: [----------] 6 tests from StructureSimilarityTest (2 ms total)
13:
13: [----------] 8 tests from ExponentialMovingAverage
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (1 ms)
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
13: [----------] 8 tests from ExponentialMovingAverage (2 ms total)
13:
13: [----------] 21 tests from FunctionTest
13: [ RUN ] FunctionTest.StaticLog2
13: [ OK ] FunctionTest.StaticLog2 (0 ms)
13: [ RUN ] FunctionTest.Log2I32Bit
13: [ OK ] FunctionTest.Log2I32Bit (1 ms)
13: [ RUN ] FunctionTest.Log2I64Bit
13: [ OK ] FunctionTest.Log2I64Bit (2 ms)
13: [ RUN ] FunctionTest.GreatestCommonDivisor
13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
13: [ RUN ] FunctionTest.InvsqrtFloat
13: [ OK ] FunctionTest.InvsqrtFloat (1 ms)
13: [ RUN ] FunctionTest.InvsqrtDouble
13: [ OK ] FunctionTest.InvsqrtDouble (1 ms)
13: [ RUN ] FunctionTest.InvsqrtInteger
13: [ OK ] FunctionTest.InvsqrtInteger (1 ms)
13: [ RUN ] FunctionTest.InvcbrtFloat
13: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvcbrtDouble
13: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvcbrtInteger
13: [ OK ] FunctionTest.InvcbrtInteger (1 ms)
13: [ RUN ] FunctionTest.SixthrootFloat
13: [ OK ] FunctionTest.SixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.SixthrootDouble
13: [ OK ] FunctionTest.SixthrootDouble (1 ms)
13: [ RUN ] FunctionTest.SixthrootInteger
13: [ OK ] FunctionTest.SixthrootInteger (1 ms)
13: [ RUN ] FunctionTest.InvsixthrootFloat
13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootDouble
13: [ OK ] FunctionTest.InvsixthrootDouble (1 ms)
13: [ RUN ] FunctionTest.InvsixthrootInteger
13: [ OK ] FunctionTest.InvsixthrootInteger (1 ms)
13: [ RUN ] FunctionTest.Powers
13: [ OK ] FunctionTest.Powers (0 ms)
13: [ RUN ] FunctionTest.ErfInvFloat
13: [ OK ] FunctionTest.ErfInvFloat (0 ms)
13: [ RUN ] FunctionTest.ErfInvDouble
13: [ OK ] FunctionTest.ErfInvDouble (1 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
13: [----------] 21 tests from FunctionTest (16 ms total)
13:
13: [----------] 4 tests from GaussianOn1DLattice
13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
13: [ RUN ] GaussianOn1DLattice.isCorrect
13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (1 ms)
13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
13: [----------] 4 tests from GaussianOn1DLattice (1 ms total)
13:
13: [----------] 9 tests from GaussTransformTest
13: [ RUN ] GaussTransformTest.isZeroUponConstruction
13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (1 ms)
13: [ RUN ] GaussTransformTest.view
13: [ OK ] GaussTransformTest.view (0 ms)
13: [----------] 9 tests from GaussTransformTest (1 ms total)
13:
13: [----------] 3 tests from DensityFittingForce
13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (1 ms)
13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (0 ms)
13: [ RUN ] DensityFittingForce.pullsTowardsDerivative
13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
13: [----------] 3 tests from DensityFittingForce (1 ms total)
13:
13: [----------] 2 tests from InvertMatrixTest
13: [ RUN ] InvertMatrixTest.IdentityIsImpotent
13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertMatrixTest.ComputesInverse
13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
13: [----------] 2 tests from InvertMatrixTest (0 ms total)
13:
13: [----------] 2 tests from InvertBoxMatrixTest
13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
13:
13: [----------] 15 tests from MatrixTest
13: [ RUN ] MatrixTest.canSetFromArray
13: [ OK ] MatrixTest.canSetFromArray (0 ms)
13: [ RUN ] MatrixTest.canSetStaticallyFromList
13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
13: [ RUN ] MatrixTest.canConstructAndFill
13: [ OK ] MatrixTest.canConstructAndFill (0 ms)
13: [ RUN ] MatrixTest.canSetValues
13: [ OK ] MatrixTest.canSetValues (0 ms)
13: [ RUN ] MatrixTest.canCopyAssign
13: [ OK ] MatrixTest.canCopyAssign (0 ms)
13: [ RUN ] MatrixTest.canSwap
13: [ OK ] MatrixTest.canSwap (1 ms)
13: [ RUN ] MatrixTest.staticMultiDimArrayExtent
13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MatrixTest.determinantWorks
13: [ OK ] MatrixTest.determinantWorks (0 ms)
13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
13: [ RUN ] MatrixTest.traceWorks
13: [ OK ] MatrixTest.traceWorks (0 ms)
13: [ RUN ] MatrixTest.transposeWorks
13: [ OK ] MatrixTest.transposeWorks (0 ms)
13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
13: [ RUN ] MatrixTest.canFillLegacyMatrix
13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
13: [----------] 15 tests from MatrixTest (1 ms total)
13:
13: [----------] 25 tests from MultiDimArrayTest
13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapStatic
13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapDynamic
13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToView
13: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToConstView
13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
13: [ RUN ] MultiDimArrayTest.viewBegin
13: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.viewEnd
13: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstBegin
13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstEnd
13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
13: [----------] 25 tests from MultiDimArrayTest (1 ms total)
13:
13: [----------] 4 tests from MultiDimArrayToMdSpanTest
13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanCopyAssign
13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanMoveAssign
13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanSwap
13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanCopyAssign
13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanMoveAssign
13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanSwap
13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanCopyAssign
13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanMoveAssign
13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanSwap
13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/2 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanCopyAssign
13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanMoveAssign
13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanSwap
13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanCopyAssign
13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanMoveAssign
13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanSwap
13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/4 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanCopyAssign
13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanMoveAssign
13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanSwap
13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/5 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanCopyAssign
13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanMoveAssign
13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanSwap
13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanCopyAssign
13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanMoveAssign
13: [ OK ] PaddedVectorTest/7.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanSwap
13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/7 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanCopyAssign
13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanMoveAssign
13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanSwap
13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanCopyAssign
13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanMoveAssign
13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanSwap
13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
13:
13: [----------] 37 tests from RVecTest
13: [ RUN ] RVecTest.CanBeStoredInVector
13: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAsMutable_rvec
13: [ OK ] RVecTest.WorksAsMutable_rvec (1 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Array
13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
13: [ RUN ] RVecTest.CanAddRVecToRvec
13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanAddAssignRVecToRvec
13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractRVecFromRvec
13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanDotProductRVecByRvec
13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanCrossProductRVecByRvec
13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVecInplace
13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
13: [ RUN ] RVecTest.CanScaleRVec
13: [ OK ] RVecTest.CanScaleRVec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVec
13: [ OK ] RVecTest.CanDivideRVec (0 ms)
13: [ RUN ] RVecTest.CanDoUnitvFromRVec
13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanSqLengthOfRVec
13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanLengthOfRVec
13: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToRVec
13: [ OK ] RVecTest.CanCastToRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToDVec
13: [ OK ] RVecTest.CanCastToDVec (0 ms)
13: [ RUN ] RVecTest.CanLeftScalarMultiply
13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanRightScalarMultiply
13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanGetUnitvFromRVec
13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanGetSqLengthOfRVec
13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanGetLengthOfRVec
13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoCrossProductOfRVec
13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoDotProductOfRVec
13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanScaleByVector
13: [ OK ] RVecTest.CanScaleByVector (1 ms)
13: [ RUN ] RVecTest.asIVec
13: [ OK ] RVecTest.asIVec (0 ms)
13: [ RUN ] RVecTest.elementWiseMin
13: [ OK ] RVecTest.elementWiseMin (0 ms)
13: [ RUN ] RVecTest.elementWiseMax
13: [ OK ] RVecTest.elementWiseMax (0 ms)
13: [ RUN ] RVecTest.WorksAs_dvec_Reference
13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_ivec_Reference
13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Reference
13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
13: [ RUN ] RVecTest.CopyConstructorWorks
13: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
13: [ RUN ] RVecTest.CopyAssignmentWorks
13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
13: [ RUN ] RVecTest.MoveConstructorWorks
13: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
13: [ RUN ] RVecTest.MoveAssignmentWorks
13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
13: [----------] 37 tests from RVecTest (2 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 204 tests from 29 test cases ran. (425 ms total)
13: [ PASSED ] 204 tests.
13/54 Test #13: MathUnitTests ....................... Passed 0.51 sec
test 14
Start 14: MdrunUtilityUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 17 tests from 1 test case.
14: [----------] Global test environment set-up.
14: [----------] 17 tests from ThreadAffinityTest
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (2 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
14: NOTE: Affinity setting failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (2 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
14: NOTE: Affinity setting for 1/2 threads failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (2 ms)
14: [----------] 17 tests from ThreadAffinityTest (17 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 17 tests from 1 test case ran. (17 ms total)
14: [ PASSED ] 17 tests.
14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.08 sec
test 15
Start 15: MdrunUtilityMpiUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 13 tests from 2 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from ThreadAffinityMultiRankTest
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (10 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (6 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (5 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (9 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
15: [----------] 6 tests from ThreadAffinityMultiRankTest (35 ms total)
15:
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (6 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (4 ms)
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (31 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 13 tests from 2 test cases ran. (66 ms total)
15: [ PASSED ] 13 tests.
15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 0.17 sec
test 16
Start 16: MDSpanTests
16: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MDSpanTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 32 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 4 tests from BasicAccessorPolicy
16: [ RUN ] BasicAccessorPolicy.Decay
16: [ OK ] BasicAccessorPolicy.Decay (0 ms)
16: [ RUN ] BasicAccessorPolicy.Access
16: [ OK ] BasicAccessorPolicy.Access (0 ms)
16: [ RUN ] BasicAccessorPolicy.Offset
16: [ OK ] BasicAccessorPolicy.Offset (0 ms)
16: [ RUN ] BasicAccessorPolicy.CopyAccessor
16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
16: [----------] 4 tests from BasicAccessorPolicy (0 ms total)
16:
16: [----------] 4 tests from ExtentsTest
16: [ RUN ] ExtentsTest.Construction
16: [ OK ] ExtentsTest.Construction (0 ms)
16: [ RUN ] ExtentsTest.PurelyStatic
16: [ OK ] ExtentsTest.PurelyStatic (0 ms)
16: [ RUN ] ExtentsTest.RankNought
16: [ OK ] ExtentsTest.RankNought (0 ms)
16: [ RUN ] ExtentsTest.Assignment
16: [ OK ] ExtentsTest.Assignment (0 ms)
16: [----------] 4 tests from ExtentsTest (0 ms total)
16:
16: [----------] 8 tests from MdSpanExtension
16: [ RUN ] MdSpanExtension.SlicingAllStatic
16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingDynamic
16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingAllStatic3D
16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
16: [ RUN ] MdSpanExtension.SlicingEqualsView3D
16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
16: [ RUN ] MdSpanExtension.additionWorks
16: [ OK ] MdSpanExtension.additionWorks (0 ms)
16: [ RUN ] MdSpanExtension.subtractionWorks
16: [ OK ] MdSpanExtension.subtractionWorks (1 ms)
16: [ RUN ] MdSpanExtension.multiplicationWorks
16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
16: [ RUN ] MdSpanExtension.divisionWorks
16: [ OK ] MdSpanExtension.divisionWorks (0 ms)
16: [----------] 8 tests from MdSpanExtension (1 ms total)
16:
16: [----------] 3 tests from LayoutTests
16: [ RUN ] LayoutTests.LayoutRightConstruction
16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
16: [ RUN ] LayoutTests.LayoutRightProperties
16: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
16: [ RUN ] LayoutTests.LayoutRightOperator
16: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
16: [----------] 3 tests from LayoutTests (0 ms total)
16:
16: [----------] 1 test from MdSpanTest
16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
16: [----------] 1 test from MdSpanTest (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
16: [ RUN ] MdSpanTest/0.Rank
16: [ OK ] MdSpanTest/0.Rank (0 ms)
16: [ RUN ] MdSpanTest/0.DynamicRank
16: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/0.Extents
16: [ OK ] MdSpanTest/0.Extents (0 ms)
16: [ RUN ] MdSpanTest/0.Strides
16: [ OK ] MdSpanTest/0.Strides (0 ms)
16: [ RUN ] MdSpanTest/0.Properties
16: [ OK ] MdSpanTest/0.Properties (0 ms)
16: [ RUN ] MdSpanTest/0.Operator
16: [ OK ] MdSpanTest/0.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/0 (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
16: [ RUN ] MdSpanTest/1.Rank
16: [ OK ] MdSpanTest/1.Rank (0 ms)
16: [ RUN ] MdSpanTest/1.DynamicRank
16: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/1.Extents
16: [ OK ] MdSpanTest/1.Extents (0 ms)
16: [ RUN ] MdSpanTest/1.Strides
16: [ OK ] MdSpanTest/1.Strides (0 ms)
16: [ RUN ] MdSpanTest/1.Properties
16: [ OK ] MdSpanTest/1.Properties (0 ms)
16: [ RUN ] MdSpanTest/1.Operator
16: [ OK ] MdSpanTest/1.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/1 (1 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 32 tests from 7 test cases ran. (3 ms total)
16: [ PASSED ] 32 tests.
16/54 Test #16: MDSpanTests ......................... Passed 0.07 sec
test 17
Start 17: OnlineHelpUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OnlineHelpUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 22 tests from 4 test cases.
17: [----------] Global test environment set-up.
17: [----------] 6 tests from TextTableFormatterTest
17: [ RUN ] TextTableFormatterTest.HandlesBasicCase
17: [ OK ] TextTableFormatterTest.HandlesBasicCase (26 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesIndentation
17: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (2 ms)
17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (1 ms)
17: [----------] 6 tests from TextTableFormatterTest (31 ms total)
17:
17: [----------] 3 tests from HelpManagerTest
17: [ RUN ] HelpManagerTest.HandlesRootTopic
17: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
17: [ RUN ] HelpManagerTest.HandlesSubTopics
17: [ OK ] HelpManagerTest.HandlesSubTopics (0 ms)
17: [ RUN ] HelpManagerTest.HandlesInvalidTopics
17: [ OK ] HelpManagerTest.HandlesInvalidTopics (1 ms)
17: [----------] 3 tests from HelpManagerTest (2 ms total)
17:
17: [----------] 2 tests from HelpTopicFormattingTest
17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (1 ms)
17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
17: [----------] 2 tests from HelpTopicFormattingTest (2 ms total)
17:
17: [----------] 11 tests from HelpWriterContextTest
17: [ RUN ] HelpWriterContextTest.FormatsParagraphs
17: [ OK ] HelpWriterContextTest.FormatsParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (1 ms)
17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralText
17: [ OK ] HelpWriterContextTest.FormatsLiteralText (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsBulletList
17: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsGridTable
17: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsTitles
17: [ OK ] HelpWriterContextTest.FormatsTitles (1 ms)
17: [----------] 11 tests from HelpWriterContextTest (8 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 22 tests from 4 test cases ran. (43 ms total)
17: [ PASSED ] 22 tests.
17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.11 sec
test 18
Start 18: OptionsUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/OptionsUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 110 tests from 18 test cases.
18: [----------] Global test environment set-up.
18: [----------] 5 tests from AbstractOptionStorageTest
18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (1 ms)
18: [----------] 5 tests from AbstractOptionStorageTest (4 ms total)
18:
18: [----------] 8 tests from FileNameOptionTest
18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (1 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
18: [----------] 8 tests from FileNameOptionTest (1 ms total)
18:
18: [----------] 15 tests from FileNameOptionManagerTest
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (1 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
18: [----------] 15 tests from FileNameOptionManagerTest (3 ms total)
18:
18: [----------] 1 test from OptionsTest
18: [ RUN ] OptionsTest.FailsOnNonsafeStorage
18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
18: [----------] 1 test from OptionsTest (0 ms total)
18:
18: [----------] 9 tests from OptionsAssignerTest
18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (1 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMissingValue
18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesExtraValue
18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesGroups
18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesSections
18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
18: [----------] 9 tests from OptionsAssignerTest (1 ms total)
18:
18: [----------] 4 tests from OptionsAssignerBooleanTest
18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (1 ms)
18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
18: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
18:
18: [----------] 13 tests from OptionsAssignerIntegerTest
18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (1 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
18: [----------] 13 tests from OptionsAssignerIntegerTest (2 ms total)
18:
18: [----------] 5 tests from OptionsAssignerDoubleTest
18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
18: [----------] 5 tests from OptionsAssignerDoubleTest (0 ms total)
18:
18: [----------] 9 tests from OptionsAssignerStringTest
18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (1 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
18:
18: [----------] 6 tests from OptionsAssignerEnumTest
18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 6 tests from OptionsAssignerEnumTest (1 ms total)
18:
18: [----------] 8 tests from RepeatingOptionSectionTest
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (1 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
18: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
18:
18: [----------] 1 test from TimeUnitManagerTest
18: [ RUN ] TimeUnitManagerTest.BasicOperations
18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
18: [----------] 1 test from TimeUnitManagerTest (0 ms total)
18:
18: [----------] 4 tests from TimeUnitBehaviorTest
18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (1 ms)
18: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
18:
18: [----------] 2 tests from TreeValueSupportAssignTest
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
18:
18: [----------] 1 test from TreeValueSupportAssignErrorTest
18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (0 ms)
18: [----------] 1 test from TreeValueSupportAssignErrorTest (0 ms total)
18:
18: [----------] 5 tests from TreeValueSupportCheckTest
18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
18:
18: [----------] 6 tests from TreeValueSupportAdjustTest
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (9 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (2 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (2 ms)
18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (1 ms)
18: [----------] 6 tests from TreeValueSupportAdjustTest (14 ms total)
18:
18: [----------] 8 tests from TreeValueSupportTest
18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsInt64Option
18: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsStringOption
18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsFloatOption
18: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumOption
18: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
18: [----------] 8 tests from TreeValueSupportTest (7 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 110 tests from 18 test cases ran. (38 ms total)
18: [ PASSED ] 110 tests.
18/54 Test #18: OptionsUnitTests .................... Passed 0.17 sec
test 19
Start 19: PbcutilUnitTest
19: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PbcutilUnitTest.xml"
19: Test timeout computed to be: 30
19: [==========] Running 3 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 1 test from PbcTest
19: [ RUN ] PbcTest.CalcShiftsWorks
19: [ OK ] PbcTest.CalcShiftsWorks (21 ms)
19: [----------] 1 test from PbcTest (21 ms total)
19:
19: [----------] 2 tests from PbcEnumsTest
19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
19: [----------] 2 tests from PbcEnumsTest (0 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 3 tests from 2 test cases ran. (22 ms total)
19: [ PASSED ] 3 tests.
19/54 Test #19: PbcutilUnitTest ..................... Passed 0.08 sec
test 20
Start 20: RandomUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RandomUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 44 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 4 tests from ExponentialDistributionTest
20: [ RUN ] ExponentialDistributionTest.Output
20: [ OK ] ExponentialDistributionTest.Output (29 ms)
20: [ RUN ] ExponentialDistributionTest.Logical
20: [ OK ] ExponentialDistributionTest.Logical (0 ms)
20: [ RUN ] ExponentialDistributionTest.Reset
20: [ OK ] ExponentialDistributionTest.Reset (0 ms)
20: [ RUN ] ExponentialDistributionTest.AltParam
20: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from ExponentialDistributionTest (30 ms total)
20:
20: [----------] 4 tests from GammaDistributionTest
20: [ RUN ] GammaDistributionTest.Output
20: [ OK ] GammaDistributionTest.Output (2 ms)
20: [ RUN ] GammaDistributionTest.Logical
20: [ OK ] GammaDistributionTest.Logical (0 ms)
20: [ RUN ] GammaDistributionTest.Reset
20: [ OK ] GammaDistributionTest.Reset (0 ms)
20: [ RUN ] GammaDistributionTest.AltParam
20: [ OK ] GammaDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from GammaDistributionTest (3 ms total)
20:
20: [----------] 4 tests from NormalDistributionTest
20: [ RUN ] NormalDistributionTest.Output
20: [ OK ] NormalDistributionTest.Output (1 ms)
20: [ RUN ] NormalDistributionTest.Logical
20: [ OK ] NormalDistributionTest.Logical (0 ms)
20: [ RUN ] NormalDistributionTest.Reset
20: [ OK ] NormalDistributionTest.Reset (0 ms)
20: [ RUN ] NormalDistributionTest.AltParam
20: [ OK ] NormalDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from NormalDistributionTest (2 ms total)
20:
20: [----------] 1 test from SeedTest
20: [ RUN ] SeedTest.makeRandomSeed
20: [ OK ] SeedTest.makeRandomSeed (19 ms)
20: [----------] 1 test from SeedTest (19 ms total)
20:
20: [----------] 6 tests from TabulatedNormalDistributionTest
20: [ RUN ] TabulatedNormalDistributionTest.Output14
20: [ OK ] TabulatedNormalDistributionTest.Output14 (1 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Output16
20: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (1 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Logical
20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Reset
20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.AltParam
20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
20: [----------] 6 tests from TabulatedNormalDistributionTest (4 ms total)
20:
20: [----------] 1 test from TabulatedNormalDistributionTableTest
20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (8 ms)
20: [----------] 1 test from TabulatedNormalDistributionTableTest (9 ms total)
20:
20: [----------] 6 tests from ThreeFry2x64Test
20: [ RUN ] ThreeFry2x64Test.Logical
20: [ OK ] ThreeFry2x64Test.Logical (0 ms)
20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
20: [ RUN ] ThreeFry2x64Test.Reseed
20: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
20: [ RUN ] ThreeFry2x64Test.Discard
20: [ OK ] ThreeFry2x64Test.Discard (0 ms)
20: [ RUN ] ThreeFry2x64Test.InvalidCounter
20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
20: [----------] 6 tests from ThreeFry2x64Test (3 ms total)
20:
20: [----------] 4 tests from UniformIntDistributionTest
20: [ RUN ] UniformIntDistributionTest.Output
20: [ OK ] UniformIntDistributionTest.Output (1 ms)
20: [ RUN ] UniformIntDistributionTest.Logical
20: [ OK ] UniformIntDistributionTest.Logical (0 ms)
20: [ RUN ] UniformIntDistributionTest.Reset
20: [ OK ] UniformIntDistributionTest.Reset (0 ms)
20: [ RUN ] UniformIntDistributionTest.AltParam
20: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from UniformIntDistributionTest (2 ms total)
20:
20: [----------] 5 tests from UniformRealDistributionTest
20: [ RUN ] UniformRealDistributionTest.GenerateCanonical
20: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
20: [ RUN ] UniformRealDistributionTest.Output
20: [ OK ] UniformRealDistributionTest.Output (1 ms)
20: [ RUN ] UniformRealDistributionTest.Logical
20: [ OK ] UniformRealDistributionTest.Logical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Reset
20: [ OK ] UniformRealDistributionTest.Reset (0 ms)
20: [ RUN ] UniformRealDistributionTest.AltParam
20: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
20: [----------] 5 tests from UniformRealDistributionTest (3 ms total)
20:
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (1 ms)
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (7 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 44 tests from 10 test cases ran. (82 ms total)
20: [ PASSED ] 44 tests.
20/54 Test #20: RandomUnitTests ..................... Passed 0.19 sec
test 21
Start 21: RestraintTests
21: Test command: /<<PKGBUILDDIR>>/build/basic/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/RestraintTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 1 test from 1 test case.
21: [----------] Global test environment set-up.
21: [----------] 1 test from RestraintManager
21: [ RUN ] RestraintManager.restraintList
21: [ OK ] RestraintManager.restraintList (0 ms)
21: [----------] 1 test from RestraintManager (0 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 1 test from 1 test case ran. (1 ms total)
21: [ PASSED ] 1 test.
21/54 Test #21: RestraintTests ...................... Passed 0.06 sec
test 22
Start 22: TableUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TableUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 16 tests from 2 test cases.
22: [----------] Global test environment set-up.
22: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (8 ms)
22: [ RUN ] SplineTableTest/0.Sinc
22: [ OK ] SplineTableTest/0.Sinc (5 ms)
22: [ RUN ] SplineTableTest/0.LJ12
22: [ OK ] SplineTableTest/0.LJ12 (80 ms)
22: [ RUN ] SplineTableTest/0.PmeCorrection
22: [ OK ] SplineTableTest/0.PmeCorrection (8 ms)
22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (7 ms)
22: [ RUN ] SplineTableTest/0.TwoFunctions
22: [ OK ] SplineTableTest/0.TwoFunctions (161 ms)
22: [ RUN ] SplineTableTest/0.ThreeFunctions
22: [ OK ] SplineTableTest/0.ThreeFunctions (188 ms)
22: [----------] 8 tests from SplineTableTest/0 (459 ms total)
22:
22: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (7 ms)
22: [ RUN ] SplineTableTest/1.Sinc
22: [ OK ] SplineTableTest/1.Sinc (3 ms)
22: [ RUN ] SplineTableTest/1.LJ12
22: [ OK ] SplineTableTest/1.LJ12 (12 ms)
22: [ RUN ] SplineTableTest/1.PmeCorrection
22: [ OK ] SplineTableTest/1.PmeCorrection (8 ms)
22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (1 ms)
22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (6 ms)
22: [ RUN ] SplineTableTest/1.TwoFunctions
22: [ OK ] SplineTableTest/1.TwoFunctions (23 ms)
22: [ RUN ] SplineTableTest/1.ThreeFunctions
22: [ OK ] SplineTableTest/1.ThreeFunctions (27 ms)
22: [----------] 8 tests from SplineTableTest/1 (88 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 16 tests from 2 test cases ran. (547 ms total)
22: [ PASSED ] 16 tests.
22/54 Test #22: TableUnitTests ...................... Passed 0.61 sec
test 23
Start 23: TaskAssignmentUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TaskAssignmentUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 3 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (2 ms)
23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (2 ms total)
23:
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms)
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 3 tests from 2 test cases ran. (4 ms total)
23: [ PASSED ] 3 tests.
23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.07 sec
test 24
Start 24: TopologyTest
24: Test command: /<<PKGBUILDDIR>>/build/basic/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TopologyTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 11 tests from 3 test cases.
24: [----------] Global test environment set-up.
24: [----------] 3 tests from ExclusionBlockTest
24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
24: [ RUN ] ExclusionBlockTest.MergeExclusions
24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
24: [----------] 3 tests from ExclusionBlockTest (0 ms total)
24:
24: [----------] 2 tests from MtopTest
24: [ RUN ] MtopTest.RangeBasedLoop
24: [ OK ] MtopTest.RangeBasedLoop (0 ms)
24: [ RUN ] MtopTest.Operators
24: [ OK ] MtopTest.Operators (1 ms)
24: [----------] 2 tests from MtopTest (1 ms total)
24:
24: [----------] 6 tests from SymtabTest
24: [ RUN ] SymtabTest.EmptyOnOpen
24: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
24: [ RUN ] SymtabTest.AddSingleEntry
24: [ OK ] SymtabTest.AddSingleEntry (0 ms)
24: [ RUN ] SymtabTest.AddTwoDistinctEntries
24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
24: [ RUN ] SymtabTest.TryToAddDuplicates
24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms)
24: [ RUN ] SymtabTest.AddLargeNumberOfEntries
24: [ OK ] SymtabTest.AddLargeNumberOfEntries (1 ms)
24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (1 ms)
24: [----------] 6 tests from SymtabTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 11 tests from 3 test cases ran. (4 ms total)
24: [ PASSED ] 11 tests.
24/54 Test #24: TopologyTest ........................ Passed 0.07 sec
test 25
Start 25: PullTest
25: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/PullTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 5 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 5 tests from PullTest
25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
25: [----------] 5 tests from PullTest (0 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 5 tests from 1 test case ran. (1 ms total)
25: [ PASSED ] 5 tests.
25/54 Test #25: PullTest ............................ Passed 0.06 sec
test 26
Start 26: AwhTest
26: Test command: /<<PKGBUILDDIR>>/build/basic/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AwhTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 12 tests from 4 test cases.
26: [----------] Global test environment set-up.
26: [----------] 1 test from BiasTest
26: [ RUN ] BiasTest.DetectsCovering
26: [ OK ] BiasTest.DetectsCovering (8 ms)
26: [----------] 1 test from BiasTest (8 ms total)
26:
26: [----------] 1 test from gridTest
26: [ RUN ] gridTest.neighborhood
26: [ OK ] gridTest.neighborhood (10 ms)
26: [----------] 1 test from gridTest (10 ms total)
26:
26: [----------] 8 tests from WithParameters/BiasTest
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (42 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (14 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (3 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (12 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (4 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (3 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (3 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (5 ms)
26: [----------] 8 tests from WithParameters/BiasTest (88 ms total)
26:
26: [----------] 2 tests from WithParameters/BiasStateTest
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (7 ms)
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (2 ms)
26: [----------] 2 tests from WithParameters/BiasStateTest (9 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 12 tests from 4 test cases ran. (115 ms total)
26: [ PASSED ] 12 tests.
26/54 Test #26: AwhTest ............................. Passed 0.18 sec
test 27
Start 27: SimdUnitTests
27: Test command: /<<PKGBUILDDIR>>/build/basic/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SimdUnitTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 86 tests from 3 test cases.
27: [----------] Global test environment set-up.
27: [----------] 41 tests from SimdScalarTest
27: [ RUN ] SimdScalarTest.load
27: [ OK ] SimdScalarTest.load (0 ms)
27: [ RUN ] SimdScalarTest.loadU
27: [ OK ] SimdScalarTest.loadU (0 ms)
27: [ RUN ] SimdScalarTest.store
27: [ OK ] SimdScalarTest.store (0 ms)
27: [ RUN ] SimdScalarTest.storeU
27: [ OK ] SimdScalarTest.storeU (0 ms)
27: [ RUN ] SimdScalarTest.setZero
27: [ OK ] SimdScalarTest.setZero (0 ms)
27: [ RUN ] SimdScalarTest.andNot
27: [ OK ] SimdScalarTest.andNot (0 ms)
27: [ RUN ] SimdScalarTest.fma
27: [ OK ] SimdScalarTest.fma (0 ms)
27: [ RUN ] SimdScalarTest.fms
27: [ OK ] SimdScalarTest.fms (0 ms)
27: [ RUN ] SimdScalarTest.fnma
27: [ OK ] SimdScalarTest.fnma (0 ms)
27: [ RUN ] SimdScalarTest.fnms
27: [ OK ] SimdScalarTest.fnms (0 ms)
27: [ RUN ] SimdScalarTest.maskAdd
27: [ OK ] SimdScalarTest.maskAdd (0 ms)
27: [ RUN ] SimdScalarTest.maskzMul
27: [ OK ] SimdScalarTest.maskzMul (0 ms)
27: [ RUN ] SimdScalarTest.maskzFma
27: [ OK ] SimdScalarTest.maskzFma (0 ms)
27: [ RUN ] SimdScalarTest.abs
27: [ OK ] SimdScalarTest.abs (0 ms)
27: [ RUN ] SimdScalarTest.max
27: [ OK ] SimdScalarTest.max (0 ms)
27: [ RUN ] SimdScalarTest.min
27: [ OK ] SimdScalarTest.min (0 ms)
27: [ RUN ] SimdScalarTest.round
27: [ OK ] SimdScalarTest.round (0 ms)
27: [ RUN ] SimdScalarTest.trunc
27: [ OK ] SimdScalarTest.trunc (0 ms)
27: [ RUN ] SimdScalarTest.reduce
27: [ OK ] SimdScalarTest.reduce (0 ms)
27: [ RUN ] SimdScalarTest.testBits
27: [ OK ] SimdScalarTest.testBits (0 ms)
27: [ RUN ] SimdScalarTest.anyTrue
27: [ OK ] SimdScalarTest.anyTrue (0 ms)
27: [ RUN ] SimdScalarTest.selectByMask
27: [ OK ] SimdScalarTest.selectByMask (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMask
27: [ OK ] SimdScalarTest.selectByNotMask (0 ms)
27: [ RUN ] SimdScalarTest.blend
27: [ OK ] SimdScalarTest.blend (0 ms)
27: [ RUN ] SimdScalarTest.cvtR2I
27: [ OK ] SimdScalarTest.cvtR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvttR2I
27: [ OK ] SimdScalarTest.cvttR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvtI2R
27: [ OK ] SimdScalarTest.cvtI2R (0 ms)
27: [ RUN ] SimdScalarTest.cvtF2D
27: [ OK ] SimdScalarTest.cvtF2D (0 ms)
27: [ RUN ] SimdScalarTest.cvtD2D
27: [ OK ] SimdScalarTest.cvtD2D (0 ms)
27: [ RUN ] SimdScalarTest.loadI
27: [ OK ] SimdScalarTest.loadI (0 ms)
27: [ RUN ] SimdScalarTest.loadUI
27: [ OK ] SimdScalarTest.loadUI (0 ms)
27: [ RUN ] SimdScalarTest.storeI
27: [ OK ] SimdScalarTest.storeI (0 ms)
27: [ RUN ] SimdScalarTest.storeUI
27: [ OK ] SimdScalarTest.storeUI (0 ms)
27: [ RUN ] SimdScalarTest.andNotI
27: [ OK ] SimdScalarTest.andNotI (0 ms)
27: [ RUN ] SimdScalarTest.testBitsI
27: [ OK ] SimdScalarTest.testBitsI (0 ms)
27: [ RUN ] SimdScalarTest.selectByMaskI
27: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMaskI
27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
27: [ RUN ] SimdScalarTest.blendI
27: [ OK ] SimdScalarTest.blendI (0 ms)
27: [ RUN ] SimdScalarTest.cvtB2IB
27: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
27: [ RUN ] SimdScalarTest.cvtIB2B
27: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
27: [ RUN ] SimdScalarTest.expandScalarsToTriplets
27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
27: [----------] 41 tests from SimdScalarTest (2 ms total)
27:
27: [----------] 8 tests from SimdScalarUtilTest
27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
27: [----------] 8 tests from SimdScalarUtilTest (1 ms total)
27:
27: [----------] 37 tests from SimdScalarMathTest
27: [ RUN ] SimdScalarMathTest.copysign
27: [ OK ] SimdScalarMathTest.copysign (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPair
27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
27: [ RUN ] SimdScalarMathTest.inv
27: [ OK ] SimdScalarMathTest.inv (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrt
27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
27: [ RUN ] SimdScalarMathTest.log
27: [ OK ] SimdScalarMathTest.log (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2
27: [ OK ] SimdScalarMathTest.exp2 (0 ms)
27: [ RUN ] SimdScalarMathTest.exp
27: [ OK ] SimdScalarMathTest.exp (0 ms)
27: [ RUN ] SimdScalarMathTest.erf
27: [ OK ] SimdScalarMathTest.erf (0 ms)
27: [ RUN ] SimdScalarMathTest.erfc
27: [ OK ] SimdScalarMathTest.erfc (0 ms)
27: [ RUN ] SimdScalarMathTest.sincos
27: [ OK ] SimdScalarMathTest.sincos (0 ms)
27: [ RUN ] SimdScalarMathTest.sin
27: [ OK ] SimdScalarMathTest.sin (0 ms)
27: [ RUN ] SimdScalarMathTest.cos
27: [ OK ] SimdScalarMathTest.cos (0 ms)
27: [ RUN ] SimdScalarMathTest.tan
27: [ OK ] SimdScalarMathTest.tan (0 ms)
27: [ RUN ] SimdScalarMathTest.asin
27: [ OK ] SimdScalarMathTest.asin (0 ms)
27: [ RUN ] SimdScalarMathTest.acos
27: [ OK ] SimdScalarMathTest.acos (0 ms)
27: [ RUN ] SimdScalarMathTest.atan
27: [ OK ] SimdScalarMathTest.atan (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2
27: [ OK ] SimdScalarMathTest.atan2 (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrection
27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.invSingleAccuracy
27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.logSingleAccuracy
27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.expSingleAccuracy
27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
27: [----------] 37 tests from SimdScalarMathTest (1 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 86 tests from 3 test cases ran. (5 ms total)
27: [ PASSED ] 86 tests.
27/54 Test #27: SimdUnitTests ....................... Passed 0.08 sec
test 28
Start 28: CompatibilityHelpersTests
28: Test command: /<<PKGBUILDDIR>>/build/basic/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CompatibilityHelpersTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 170 tests from 12 test cases.
28: [----------] Global test environment set-up.
28: [----------] 45 tests from OptionalTest
28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructEmpty
28: [ OK ] OptionalTest.CanDefaultConstructEmpty (0 ms)
28: [ RUN ] OptionalTest.CanConstructFromNullopt
28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValue
28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValue
28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromValue
28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignFromValue
28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanResetContent
28: [ OK ] OptionalTest.CanResetContent (0 ms)
28: [ RUN ] OptionalTest.ProvidesRelationalOperators
28: [ OK ] OptionalTest.ProvidesRelationalOperators (1 ms)
28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (0 ms)
28: [ RUN ] OptionalTest.CanProduceHash
28: [ OK ] OptionalTest.CanProduceHash (0 ms)
28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
28: alignment_of<char>: 1
28: alignment_of<short>: 2
28: alignment_of<int>: 4
28: alignment_of<long>: 4
28: alignment_of<float>: 4
28: alignment_of<double>: 8
28: alignment_of<long double>: 8
28: alignment_of<Struct>: 1
28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
28: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
28: sizeof( optional<char> ): 2 (1)
28: sizeof( optional<short> ): 4 (2)
28: sizeof( optional<int> ): 8 (4)
28: sizeof( optional<long> ): 8 (4)
28: sizeof( optional<float> ): 8 (4)
28: sizeof( optional<double> ): 16 (8)
28: sizeof( optional<long double> ): 16 (8)
28: sizeof( optional<Struct> ): 2 (1)
28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
28: [----------] 45 tests from OptionalTest (4 ms total)
28:
28: [----------] 7 tests from MakeOptionalTest
28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] MakeOptionalTest.CanCopyConstruct
28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanMoveConstruct
28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
28: [----------] 7 tests from MakeOptionalTest (0 ms total)
28:
28: [----------] 4 tests from OptionalMemberSwapTest
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
28:
28: [----------] 4 tests from OptionalImplicitValueTest
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (1 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
28: [----------] 4 tests from OptionalImplicitValueTest (1 ms total)
28:
28: [----------] 20 tests from OptionalIntValueTest
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (1 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (1 ms)
28: [----------] 20 tests from OptionalIntValueTest (2 ms total)
28:
28: [----------] 1 test from NotNullConstruction
28: [ RUN ] NotNullConstruction.Works
28: [ OK ] NotNullConstruction.Works (0 ms)
28: [----------] 1 test from NotNullConstruction (0 ms total)
28:
28: [----------] 1 test from NotNullCasting
28: [ RUN ] NotNullCasting.Works
28: [ OK ] NotNullCasting.Works (0 ms)
28: [----------] 1 test from NotNullCasting (0 ms total)
28:
28: [----------] 1 test from NotNullAssignment
28: [ RUN ] NotNullAssignment.Works
28: [ OK ] NotNullAssignment.Works (0 ms)
28: [----------] 1 test from NotNullAssignment (0 ms total)
28:
28: [----------] 1 test from MakeNotNull
28: [ RUN ] MakeNotNull.Works
28: [ OK ] MakeNotNull.Works (0 ms)
28: [----------] 1 test from MakeNotNull (0 ms total)
28:
28: [----------] 1 test from NotNull
28: [ RUN ] NotNull.WorksInContainers
28: [ OK ] NotNull.WorksInContainers (0 ms)
28: [----------] 1 test from NotNull (0 ms total)
28:
28: [----------] 80 tests from StringViewTest
28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromCString
28: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.AllowForwardIteration
28: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstForwardIteration
28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowReverseIteration
28: [ OK ] StringViewTest.AllowReverseIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstReverseIteration
28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaAt
28: [ OK ] StringViewTest.CanAccessElementViaAt (1 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
28: [ RUN ] StringViewTest.CanAccessAllElementsViaData
28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
28: [ RUN ] StringViewTest.CanRemovePrefix
28: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
28: [ RUN ] StringViewTest.CanRemoveSuffix
28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
28: [ RUN ] StringViewTest.CanSwapWithOtherView
28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
28: [ RUN ] StringViewTest.CanCopySubstringWithCopy
28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (1 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (1 ms)
28: [ RUN ] StringViewTest.CanCompareToViews
28: [ OK ] StringViewTest.CanCompareToViews (0 ms)
28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
28: [ RUN ] StringViewTest.CanPrintViewToPutputStream
28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
28: [----------] 80 tests from StringViewTest (6 ms total)
28:
28: [----------] 5 tests from StringViewExtensionTest
28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
28: [----------] 5 tests from StringViewExtensionTest (1 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 170 tests from 12 test cases ran. (16 ms total)
28: [ PASSED ] 170 tests.
28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.10 sec
test 29
Start 29: GmxAnaTest
29: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxAnaTest.xml"
29: Test timeout computed to be: 600
29: [==========] Running 27 tests from 5 test cases.
29: [----------] Global test environment set-up.
29: [----------] 5 tests from Entropy
29: [ RUN ] Entropy.Schlitter_300_NoLinear
29: [ OK ] Entropy.Schlitter_300_NoLinear (27 ms)
29: [ RUN ] Entropy.Schlitter_300_Linear
29: [ OK ] Entropy.Schlitter_300_Linear (2 ms)
29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (1 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_Linear
29: [ OK ] Entropy.QuasiHarmonic_200_Linear (2 ms)
29: [----------] 5 tests from Entropy (32 ms total)
29:
29: [----------] 10 tests from MindistTest
29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (67 ms)
29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (9 ms)
29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (7 ms)
29: [ RUN ] MindistTest.mindistPicksUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistPicksUpContacts (8 ms)
29: [ RUN ] MindistTest.ngWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.ngWorks (7 ms)
29: [ RUN ] MindistTest.groupWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.groupWorks (9 ms)
29: [ RUN ] MindistTest.maxDistWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.maxDistWorks (7 ms)
29: [ RUN ] MindistTest.noPbcWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.noPbcWorks (7 ms)
29: [ RUN ] MindistTest.resPerTimeWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.resPerTimeWorks (8 ms)
29: [ RUN ] MindistTest.matrixWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 5: 'atoms123'
29: Special case: making distance matrix between all atoms in group atoms123
29: [ OK ] MindistTest.matrixWorks (7 ms)
29: [----------] 10 tests from MindistTest (140 ms total)
29:
29: [----------] 3 tests from MsdTest
29: [ RUN ] MsdTest.threeDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.threeDimensionalDiffusion (9 ms)
29: [ RUN ] MsdTest.twoDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.twoDimensionalDiffusion (7 ms)
29: [ RUN ] MsdTest.oneDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.oneDimensionalDiffusion (6 ms)
29: [----------] 3 tests from MsdTest (24 ms total)
29:
29: [----------] 3 tests from MsdMolTest
29: [ RUN ] MsdMolTest.diffMolMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -9732929
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolMassWeighted (3380 ms)
29: [ RUN ] MsdMolTest.diffMolNonMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -137890003
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolNonMassWeighted (3203 ms)
29: [ RUN ] MsdMolTest.diffMolSelected
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -16779787
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( mol) has 9 elements
29: There is one group in the index
29: Split group of 9 atoms into 3 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ mol] 7.8614 (+/- 1.5618) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolSelected (3202 ms)
29: [----------] 3 tests from MsdMolTest (9788 ms total)
29:
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: trr version: GMX_trn_file (single precision)
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (41 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (9 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (18 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from gro file '', 6 atoms.
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (8 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
29:
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (9 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (8 ms)
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (93 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 27 tests from 5 test cases ran. (10077 ms total)
29: [ PASSED ] 27 tests.
29/54 Test #29: GmxAnaTest .......................... Passed 10.15 sec
test 30
Start 30: GmxPreprocessTests
30: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxPreprocessTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 69 tests from 10 test cases.
30: [----------] Global test environment set-up.
30: [----------] 4 tests from GenconfTest
30: [ RUN ] GenconfTest.nbox_Works
30: [ OK ] GenconfTest.nbox_Works (10 ms)
30: [ RUN ] GenconfTest.nbox_norenumber_Works
30: [ OK ] GenconfTest.nbox_norenumber_Works (11 ms)
30: [ RUN ] GenconfTest.nbox_dist_Works
30: [ OK ] GenconfTest.nbox_dist_Works (23 ms)
30: [ RUN ] GenconfTest.nbox_rot_Works
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: [ OK ] GenconfTest.nbox_rot_Works (18 ms)
30: [----------] 4 tests from GenconfTest (64 ms total)
30:
30: [----------] 2 tests from GenionTest
30: [ RUN ] GenionTest.HighConcentrationIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -22544529
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
30: Group 0 ( System) has 653 elements
30: Group 1 ( Water) has 648 elements
30: Group 2 ( SOL) has 648 elements
30: Group 3 ( non-Water) has 5 elements
30: Group 4 ( Other) has 5 elements
30: Group 5 ( METH) has 5 elements
30: Select a group: Number of (3-atomic) solvent molecules: 216
30: Using random seed 1997.
30: Replacing solvent molecule 56 (atom 168) with NA
30: Replacing solvent molecule 120 (atom 360) with NA
30: Replacing solvent molecule 182 (atom 546) with NA
30: Replacing solvent molecule 71 (atom 213) with NA
30: Replacing solvent molecule 189 (atom 567) with CL
30: Replacing solvent molecule 54 (atom 162) with CL
30: Replacing solvent molecule 155 (atom 465) with CL
30: Replacing solvent molecule 99 (atom 297) with CL
30:
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: Will try to add 4 NA ions and 4 CL ions.
30: Select a continuous group of solvent molecules
30: Selected 1: 'Water'
30: [ OK ] GenionTest.HighConcentrationIonPlacement (3492 ms)
30: [ RUN ] GenionTest.NoIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 1927241453
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
30: No ions to add, will just copy input configuration.
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: [ OK ] GenionTest.NoIonPlacement (3347 ms)
30: [----------] 2 tests from GenionTest (6840 ms total)
30:
30: [----------] 1 test from GenRestrTest
30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
30:
30: Reading structure file
30: Group 0 ( System) has 156 elements
30: Group 1 ( Protein) has 156 elements
30: Group 2 ( Protein-H) has 75 elements
30: Group 3 ( C-alpha) has 10 elements
30: Group 4 ( Backbone) has 30 elements
30: Group 5 ( MainChain) has 40 elements
30: Group 6 ( MainChain+Cb) has 49 elements
30: Group 7 ( MainChain+H) has 52 elements
30: Group 8 ( SideChain) has 104 elements
30: Group 9 ( SideChain-H) has 35 elements
30: Select a group: Select group to position restrain
30: Selected 3: 'C-alpha'
30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (13 ms)
30: [----------] 1 test from GenRestrTest (14 ms total)
30:
30: [----------] 9 tests from PreprocessingAtomTypesTest
30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 9 tests from PreprocessingAtomTypesTest (0 ms total)
30:
30: [----------] 10 tests from PreprocessingBondAtomTypeTest
30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (1 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 10 tests from PreprocessingBondAtomTypeTest (1 ms total)
30:
30: [----------] 5 tests from InsertMoleculesTest
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
30: Added 1 molecules (out of 1 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
30:
30: Output configuration contains 8 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (48 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3 success (now 6 atoms)!
30:
Try 4 success (now 8 atoms)!
30:
Try 5 success (now 10 atoms)!
30:
30: Added 5 molecules (out of 5 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
30:
30: Output configuration contains 10 atoms in 10 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (9 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
Try 2 success (now 10 atoms)!
30:
30: Added 2 molecules (out of 2 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
30:
30: Output configuration contains 10 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (10 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 650 atoms)!
30:
Try 2 success (now 652 atoms)!
30:
Try 3 success (now 654 atoms)!
30:
Try 4 success (now 656 atoms)!
30:
30: Added 4 molecules (out of 4 requested)
30: Replaced 8 residues (24 atoms)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
30:
30: Output configuration contains 632 atoms in 212 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (64 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
30:
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
30:
Try 13 success (now 6 atoms)!
30:
30: Added 3 molecules (out of 4 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
30:
30: Output configuration contains 6 atoms in 3 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (10 ms)
30: [----------] 5 tests from InsertMoleculesTest (141 ms total)
30:
30: [----------] 14 tests from GetIrTest
30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
30: Ignoring obsolete mdp entry 'title'
30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (29 ms)
30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (31 ms)
30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (19 ms)
30: [ RUN ] GetIrTest.RejectsValueWithoutKey
30: [ OK ] GetIrTest.RejectsValueWithoutKey (31 ms)
30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (31 ms)
30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (19 ms)
30: [ RUN ] GetIrTest.AcceptsEmptyLines
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsEmptyLines (18 ms)
30: [ RUN ] GetIrTest.AcceptsElectricField
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricField (18 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (34 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (18 ms)
30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (15 ms)
30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (20 ms)
30: [ RUN ] GetIrTest.RejectsImplicitSolventYes
30: [ OK ] GetIrTest.RejectsImplicitSolventYes (31 ms)
30: [ RUN ] GetIrTest.AcceptsMimic
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsMimic (25 ms)
30: [----------] 14 tests from GetIrTest (340 ms total)
30:
30: [----------] 5 tests from SolvateTest
30: [ RUN ] SolvateTest.cs_box_Works
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 1x1x1 boxes
30: Solvent box contains 270 atoms in 90 residues
30: Removed 129 solvent atoms due to solvent-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 47 residues
30: Generated solvent containing 141 atoms in 47 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
30:
30: Output configuration contains 141 atoms in 47 residues
30: Volume : 1.331 (nm^3)
30: Density : 1056.36 (g/l)
30: Number of solvent molecules: 47
30:
30: [ OK ] SolvateTest.cs_box_Works (199 ms)
30: [ RUN ] SolvateTest.cs_cp_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: [ OK ] SolvateTest.cs_cp_Works (290 ms)
30: [ RUN ] SolvateTest.cs_cp_p_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: Processing topology
30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
30: [ OK ] SolvateTest.cs_cp_p_Works (280 ms)
30: [ RUN ] SolvateTest.shell_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 1902 solvent atoms more than 1.000000 nm from solute.
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 252 residues
30: Generated solvent containing 756 atoms in 252 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
30:
30: Output configuration contains 762 atoms in 254 residues
30: Volume : 27.2709 (nm^3)
30: Density : 279.3 (g/l)
30: Number of solvent molecules: 252
30:
30: [ OK ] SolvateTest.shell_Works (134 ms)
30: [ RUN ] SolvateTest.update_Topology_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 3x3x3 boxes
30: Solvent box contains 14952 atoms in 4984 residues
30: Removed 2787 solvent atoms due to solvent-solvent overlap
30: Removed 30 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 2 different molecule types:
30: HOH ( 3 atoms): 1876 residues
30: SOL ( 3 atoms): 2169 residues
30: Generated solvent containing 0 atoms in 0 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
30:
30: Output configuration contains 12141 atoms in 4047 residues
30: Volume : 125 (nm^3)
30: Density : 968.963 (g/l)
30: Number of solvent molecules: 4045
30:
30: Processing topology
30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: [ OK ] SolvateTest.update_Topology_Works (1259 ms)
30: [----------] 5 tests from SolvateTest (2164 ms total)
30:
30: [----------] 1 test from TopDirTests
30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
30: [----------] 1 test from TopDirTests (0 ms total)
30:
30: [----------] 18 tests from SinglePeptideFragments/EditconfTest
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/0 (112 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/1 (40 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/2 (55 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/3 (26 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/4 (25 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/5 (27 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/6 (24 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/7 (16 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFile/8 (41 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/0 (36 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/1 (56 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/2 (32 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/3 (44 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/4 (13 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/5 (13 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/6 (22 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/7 (27 ms)
30: [ RUN ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8
30:
30: Select a group for output:
30: Group 0 ( two_residues) has 23 elements
30: There is one group in the index
30: Note that major changes are planned in future for editconf, to improve usability and utility.
30: Read 252 atoms
30: Volume: 338.104 nm^3, corresponds to roughly 152100 electrons
30: No velocities found
30: [ OK ] SinglePeptideFragments/EditconfTest.ProducesMatchingOutputStructureFileUsingIndexGroup/8 (23 ms)
30: [----------] 18 tests from SinglePeptideFragments/EditconfTest (634 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 69 tests from 10 test cases ran. (10198 ms total)
30: [ PASSED ] 69 tests.
30/54 Test #30: GmxPreprocessTests .................. Passed 10.27 sec
test 31
Start 31: Pdb2gmx1Test
31: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx1Test.xml"
31: Test timeout computed to be: 30
31: [==========] Running 24 tests from 1 test case.
31: [----------] Global test environment set-up.
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (843 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (720 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (560 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (503 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (581 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (728 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (620 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (586 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (561 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (607 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (646 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (499 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (693 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (644 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (716 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (554 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (549 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (601 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (560 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (516 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (579 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (651 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (613 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge -0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (541 ms)
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (14677 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 24 tests from 1 test case ran. (14678 ms total)
31: [ PASSED ] 24 tests.
31/54 Test #31: Pdb2gmx1Test ........................ Passed 14.75 sec
test 32
Start 32: Pdb2gmx2Test
32: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx2Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 32 tests from 2 test cases.
32: [----------] Global test environment set-up.
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (377 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (372 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (356 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (350 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (333 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (380 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (360 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (402 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (314 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (372 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (342 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (367 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (334 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (381 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (378 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (354 ms)
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (5775 ms total)
32:
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (403 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (402 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (444 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (322 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (362 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (483 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (383 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (367 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (351 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (495 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (360 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (361 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (472 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (417 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (364 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (360 ms)
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (6347 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 32 tests from 2 test cases ran. (12122 ms total)
32: [ PASSED ] 32 tests.
32/54 Test #32: Pdb2gmx2Test ........................ Passed 12.19 sec
test 33
Start 33: Pdb2gmx3Test
33: Test command: /<<PKGBUILDDIR>>/build/basic/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/Pdb2gmx3Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 28 tests from 4 test cases.
33: [----------] Global test environment set-up.
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (515 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (548 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (728 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (418 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (528 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (554 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (515 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (465 ms)
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (4274 ms total)
33:
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (498 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (509 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (449 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (417 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (480 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (541 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (506 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (455 ms)
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (3858 ms total)
33:
33: [----------] 8 tests from ChainSep/Pdb2gmxTest
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (527 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 7 acceptors were found.
33: There are 7 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS8
33: NE223
33: MET12 SD55 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 125, now 125
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 317 pairs
33: Before cleaning: 322 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 5 cmap torsion pairs
33: There are 322 dihedrals, 19 impropers, 227 angles
33: 314 pairs, 125 bonds and 0 virtual sites
33: Total mass 846.083 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 7 58
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (58 atoms, 7 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 7 residues with 124 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 124 atoms 7 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (325 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (534 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 12 acceptors were found.
33: There are 13 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3
33: SG9
33: HIS8 NE251 1.055
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 115, now 115
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 288 pairs
33: Before cleaning: 293 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 6 cmap torsion pairs
33: There are 293 dihedrals, 23 impropers, 203 angles
33: 285 pairs, 115 bonds and 0 virtual sites
33: Total mass 888.952 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 8 61
33: 2 'B' 3 25
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (61 atoms, 8 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 8 residues with 114 atoms
33: Chain time...
33: Processing chain 2 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 114 atoms 8 residues
33: Including chain 2 in system: 61 atoms 3 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (380 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 260, now 260
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 650 pairs
33: Before cleaning: 660 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 8 cmap torsion pairs
33: There are 660 dihedrals, 45 impropers, 466 angles
33: 647 pairs, 260 bonds and 0 virtual sites
33: Total mass 1900.162 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33:
33: Merged chains into joint molecule definitions at 3 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 261 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (491 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 6 donors and 4 acceptors were found.
33: There are 3 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 67, now 67
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 164 pairs
33: Before cleaning: 169 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 169 dihedrals, 13 impropers, 118 angles
33: 161 pairs, 67 bonds and 0 virtual sites
33: Total mass 472.547 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 261 atoms and 16 residues
33: Total mass in system 1900.162 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
33: They will be treated as separate chains unless you reorder your file.
33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 4 33
33: 3 'B' 3 25
33: 4 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (33 atoms, 4 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 66 atoms
33: Chain time...
33: Processing chain 3 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 4 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 66 atoms 4 residues
33: Including chain 3 in system: 61 atoms 3 residues
33: Including chain 4 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (360 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 256, now 256
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 652 pairs
33: Before cleaning: 662 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 12 cmap torsion pairs
33: There are 662 dihedrals, 47 impropers, 460 angles
33: 649 pairs, 256 bonds and 0 virtual sites
33: Total mass 1864.131 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33:
33: Merged chains into joint molecule definitions at 1 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (515 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 14 donors and 15 acceptors were found.
33: There are 20 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 173, now 173
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 441 pairs
33: Before cleaning: 446 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 9 cmap torsion pairs
33: There are 446 dihedrals, 29 impropers, 312 angles
33: 438 pairs, 173 bonds and 0 virtual sites
33: Total mass 1262.488 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 255 atoms and 16 residues
33: Total mass in system 1864.131 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 11 86
33: 2 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (86 atoms, 11 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 11 residues with 172 atoms
33: Chain time...
33: Processing chain 2 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 172 atoms 11 residues
33: Including chain 2 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (342 ms)
33: [----------] 8 tests from ChainSep/Pdb2gmxTest (3489 ms total)
33:
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (232 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (232 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (260 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge -0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (223 ms)
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (947 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 28 tests from 4 test cases ran. (12570 ms total)
33: [ PASSED ] 28 tests.
33/54 Test #33: Pdb2gmx3Test ........................ Passed 12.65 sec
test 34
Start 34: CorrelationsTest
34: Test command: /<<PKGBUILDDIR>>/build/basic/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CorrelationsTest.xml"
34: Test timeout computed to be: 30
34: [==========] Running 21 tests from 3 test cases.
34: [----------] Global test environment set-up.
34: [----------] 10 tests from AutocorrTest
34: [ RUN ] AutocorrTest.EacNormal
34: [ OK ] AutocorrTest.EacNormal (52 ms)
34: [ RUN ] AutocorrTest.EacNoNormalize
34: [ OK ] AutocorrTest.EacNoNormalize (17 ms)
34: [ RUN ] AutocorrTest.EacCos
34: [ OK ] AutocorrTest.EacCos (36 ms)
34: [ RUN ] AutocorrTest.EacVector
34: [ OK ] AutocorrTest.EacVector (68 ms)
34: [ RUN ] AutocorrTest.EacRcross
34: [ OK ] AutocorrTest.EacRcross (8 ms)
34: [ RUN ] AutocorrTest.EacP0
34: [ OK ] AutocorrTest.EacP0 (57 ms)
34: [ RUN ] AutocorrTest.EacP1
34: [ OK ] AutocorrTest.EacP1 (46 ms)
34: [ RUN ] AutocorrTest.EacP2
34: [ OK ] AutocorrTest.EacP2 (88 ms)
34: [ RUN ] AutocorrTest.EacP3
34: [ OK ] AutocorrTest.EacP3 (24 ms)
34: [ RUN ] AutocorrTest.EacP4
34: [ OK ] AutocorrTest.EacP4 (42 ms)
34: [----------] 10 tests from AutocorrTest (449 ms total)
34:
34: [----------] 1 test from ManyAutocorrelationTest
34: [ RUN ] ManyAutocorrelationTest.Empty
34: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
34: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
34:
34: [----------] 10 tests from ExpfitTest
34: [ RUN ] ExpfitTest.EffnEXP1
34: [ OK ] ExpfitTest.EffnEXP1 (4 ms)
34: [ RUN ] ExpfitTest.EffnEXP2
34: [ OK ] ExpfitTest.EffnEXP2 (6 ms)
34: [ RUN ] ExpfitTest.EffnEXPEXP
34: [ OK ] ExpfitTest.EffnEXPEXP (12 ms)
34: [ RUN ] ExpfitTest.EffnEXP5
34: [ OK ] ExpfitTest.EffnEXP5 (35 ms)
34: [ RUN ] ExpfitTest.EffnEXP7
34: [ OK ] ExpfitTest.EffnEXP7 (29 ms)
34: [ RUN ] ExpfitTest.EffnEXP9
34: [ OK ] ExpfitTest.EffnEXP9 (218 ms)
34: [ RUN ] ExpfitTest.EffnERF
34: [ OK ] ExpfitTest.EffnERF (19 ms)
34: [ RUN ] ExpfitTest.EffnERREST
34: [ OK ] ExpfitTest.EffnERREST (6 ms)
34: [ RUN ] ExpfitTest.EffnVAC
34: [ OK ] ExpfitTest.EffnVAC (40 ms)
34: [ RUN ] ExpfitTest.EffnPRES
34: [ OK ] ExpfitTest.EffnPRES (99 ms)
34: [----------] 10 tests from ExpfitTest (469 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 21 tests from 3 test cases ran. (959 ms total)
34: [ PASSED ] 21 tests.
34/54 Test #34: CorrelationsTest .................... Passed 1.02 sec
test 35
Start 35: AnalysisDataUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/AnalysisDataUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 69 tests from 14 test cases.
35: [----------] Global test environment set-up.
35: [----------] 3 tests from AnalysisDataInitializationTest
35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (2 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
35: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (35 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/0 (52 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/1 (24 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/2 (28 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/3 (29 ms total)
35:
35: [----------] 4 tests from AnalysisArrayDataTest
35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (3 ms)
35: [ RUN ] AnalysisArrayDataTest.StorageWorks
35: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
35: [----------] 4 tests from AnalysisArrayDataTest (6 ms total)
35:
35: [----------] 6 tests from AverageModuleTest
35: [ RUN ] AverageModuleTest.BasicTest
35: [ OK ] AverageModuleTest.BasicTest (18 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipointData
35: [ OK ] AverageModuleTest.HandlesMultipointData (6 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (7 ms)
35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (10 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeXAxis
35: [ OK ] AverageModuleTest.CanCustomizeXAxis (5 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (5 ms)
35: [----------] 6 tests from AverageModuleTest (52 ms total)
35:
35: [----------] 2 tests from FrameAverageModuleTest
35: [ RUN ] FrameAverageModuleTest.BasicTest
35: [ OK ] FrameAverageModuleTest.BasicTest (5 ms)
35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (6 ms)
35: [----------] 2 tests from FrameAverageModuleTest (11 ms total)
35:
35: [----------] 7 tests from AnalysisHistogramSettingsTest
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (1 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
35: [----------] 7 tests from AnalysisHistogramSettingsTest (1 ms total)
35:
35: [----------] 2 tests from SimpleHistogramModuleTest
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (8 ms)
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
35: [----------] 2 tests from SimpleHistogramModuleTest (16 ms total)
35:
35: [----------] 3 tests from WeightedHistogramModuleTest
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (8 ms)
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (8 ms)
35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (8 ms)
35: [----------] 3 tests from WeightedHistogramModuleTest (25 ms total)
35:
35: [----------] 3 tests from BinAverageModuleTest
35: [ RUN ] BinAverageModuleTest.ComputesCorrectly
35: [ OK ] BinAverageModuleTest.ComputesCorrectly (6 ms)
35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (7 ms)
35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
35: [----------] 3 tests from BinAverageModuleTest (20 ms total)
35:
35: [----------] 4 tests from AbstractAverageHistogramTest
35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (8 ms)
35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (8 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (7 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (7 ms)
35: [----------] 4 tests from AbstractAverageHistogramTest (30 ms total)
35:
35: [----------] 3 tests from LifetimeModuleTest
35: [ RUN ] LifetimeModuleTest.BasicTest
35: [ OK ] LifetimeModuleTest.BasicTest (5 ms)
35: [ RUN ] LifetimeModuleTest.CumulativeTest
35: [ OK ] LifetimeModuleTest.CumulativeTest (5 ms)
35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (6 ms)
35: [----------] 3 tests from LifetimeModuleTest (16 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 69 tests from 14 test cases ran. (313 ms total)
35: [ PASSED ] 69 tests.
35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.39 sec
test 36
Start 36: CoordinateIOTests
36: Test command: /<<PKGBUILDDIR>>/build/basic/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/CoordinateIOTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 64 tests from 19 test cases.
36: [----------] Global test environment set-up.
36: [----------] 1 test from OutputSelectorDeathTest
36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (35 ms)
36: [----------] 1 test from OutputSelectorDeathTest (35 ms total)
36:
36: [----------] 5 tests from TrajectoryFrameWriterTest
36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (30 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (25 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (23 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (47 ms)
36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
36: [----------] 5 tests from TrajectoryFrameWriterTest (126 ms total)
36:
36: [----------] 5 tests from OutputAdapterContainer
36: [ RUN ] OutputAdapterContainer.MakeEmpty
36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
36: [ RUN ] OutputAdapterContainer.AddAdapter
36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectBadAdapter
36: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (1 ms)
36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
36: [----------] 5 tests from OutputAdapterContainer (1 ms total)
36:
36: [----------] 5 tests from FlagTest
36: [ RUN ] FlagTest.CanSetSimpleFlag
36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
36: [ RUN ] FlagTest.CanAddNewBox
36: [ OK ] FlagTest.CanAddNewBox (0 ms)
36: [ RUN ] FlagTest.SetsImplicitPrecisionChange
36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitStartTimeChange
36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitTimeStepChange
36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
36: [----------] 5 tests from FlagTest (1 ms total)
36:
36: [----------] 5 tests from SetAtomsTest
36: [ RUN ] SetAtomsTest.RemovesExistingAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.RemovesExistingAtoms (27 ms)
36: [ RUN ] SetAtomsTest.AddsNewAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.AddsNewAtoms (23 ms)
36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (23 ms)
36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (23 ms)
36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (28 ms)
36: [----------] 5 tests from SetAtomsTest (124 ms total)
36:
36: [----------] 2 tests from SetBothTimeTest
36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (0 ms)
36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
36: [----------] 2 tests from SetBothTimeTest (0 ms total)
36:
36: [----------] 2 tests from SetStartTimeTest
36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (1 ms)
36: [ RUN ] SetStartTimeTest.WorksWithZeroStart
36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
36: [----------] 2 tests from SetStartTimeTest (1 ms total)
36:
36: [----------] 1 test from SetTimeStepTest
36: [ RUN ] SetTimeStepTest.SetTimeStepWorks
36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
36: [----------] 1 test from SetTimeStepTest (0 ms total)
36:
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (23 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (23 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (23 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (27 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (25 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (23 ms)
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (144 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (23 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (25 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (25 ms)
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (74 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (1 ms)
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
36:
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (48 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (49 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (48 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (48 ms)
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (193 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (24 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (25 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (25 ms)
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (74 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (25 ms)
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (29 ms)
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (55 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (1 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (23 ms)
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (23 ms)
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (47 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (1 ms)
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (1 ms total)
36:
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (27 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (24 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (23 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (24 ms)
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (98 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 64 tests from 19 test cases ran. (977 ms total)
36: [ PASSED ] 64 tests.
36/54 Test #36: CoordinateIOTests ................... Passed 1.05 sec
test 37
Start 37: TrajectoryAnalysisUnitTests
37: Test command: /<<PKGBUILDDIR>>/build/basic/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 82 tests from 16 test cases.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from ClustsizeTest
37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 2, cmax: 4, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (72 ms)
37: [ RUN ] ClustsizeTest.NoMolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 1, cmax: 6, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (30 ms)
37: [ RUN ] ClustsizeTest.MolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (30 ms)
37: [ RUN ] ClustsizeTest.MolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 1, cmax: 6, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (14 ms)
37: [ RUN ] ClustsizeTest.MolCSize
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolCSize (15 ms)
37: [----------] 5 tests from ClustsizeTest (163 ms total)
37:
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (6 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (18 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (16 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (43 ms total)
37:
37: [----------] 11 tests from AngleModuleTest
37: [ RUN ] AngleModuleTest.ComputesSimpleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesSimpleAngles (20 ms)
37: [ RUN ] AngleModuleTest.ComputesDihedrals
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesDihedrals (21 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (20 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (19 ms)
37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (19 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (19 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
37: Reading frames from gro file 'Test system for different angles', 33 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (21 ms)
37: [ RUN ] AngleModuleTest.ComputesMultipleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesMultipleAngles (20 ms)
37: [ RUN ] AngleModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesDynamicSelections (23 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (27 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (19 ms)
37: [----------] 11 tests from AngleModuleTest (231 ms total)
37:
37: [----------] 4 tests from ConvertTrjModuleTest
37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (67 ms)
37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (62 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (9 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (9 ms)
37: [----------] 4 tests from ConvertTrjModuleTest (148 ms total)
37:
37: [----------] 3 tests from DistanceModuleTest
37: [ RUN ] DistanceModuleTest.ComputesDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: [ OK ] DistanceModuleTest.ComputesDistances (23 ms)
37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
37: Number of samples: 4
37: Average distance: 1.81066 nm
37: Standard deviation: 0.79289 nm
37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (25 ms)
37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2 and res_cog x < 2.8:
37: Number of samples: 3
37: Average distance: 1.72076 nm
37: Standard deviation: 1.24839 nm
37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (28 ms)
37: [----------] 3 tests from DistanceModuleTest (78 ms total)
37:
37: [----------] 2 tests from ExtractClusterModuleTest
37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
37: trr version: GMX_trn_file (single precision)
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (28 ms)
37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (25 ms)
37: [----------] 2 tests from ExtractClusterModuleTest (55 ms total)
37:
37: [----------] 2 tests from FreeVolumeModuleTest
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for 40 particles. These were set to zero.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 13
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.02 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
37: Fractional free volume 0.194 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (732 ms)
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 17
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.48 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
37: Fractional free volume 0.200 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (689 ms)
37: [----------] 2 tests from FreeVolumeModuleTest (1423 ms total)
37:
37: [----------] 9 tests from PairDistanceModuleTest
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (23 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (20 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (19 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (19 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (20 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (20 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (20 ms)
37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (19 ms)
37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (19 ms)
37: [----------] 9 tests from PairDistanceModuleTest (181 ms total)
37:
37: [----------] 5 tests from RdfModuleTest
37: [ RUN ] RdfModuleTest.BasicTest
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.BasicTest (159 ms)
37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (154 ms)
37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (210 ms)
37: [ RUN ] RdfModuleTest.CalculatesSurf
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesSurf (96 ms)
37: [ RUN ] RdfModuleTest.CalculatesXY
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesXY (187 ms)
37: [----------] 5 tests from RdfModuleTest (811 ms total)
37:
37: [----------] 5 tests from SasaModuleTest
37: [ RUN ] SasaModuleTest.BasicTest
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.BasicTest (87 ms)
37: [ RUN ] SasaModuleTest.HandlesSelectedResidues
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesSelectedResidues (55 ms)
37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (46 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (63 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (60 ms)
37: [----------] 5 tests from SasaModuleTest (324 ms total)
37:
37: [----------] 8 tests from SelectModuleTest
37: [ RUN ] SelectModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.BasicTest (36 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (28 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (27 ms)
37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (27 ms)
37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (28 ms)
37: [ RUN ] SelectModuleTest.NormalizesSizes
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.NormalizesSizes (21 ms)
37: [ RUN ] SelectModuleTest.WritesResidueNumbers
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueNumbers (18 ms)
37: [ RUN ] SelectModuleTest.WritesResidueIndices
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueIndices (19 ms)
37: [----------] 8 tests from SelectModuleTest (209 ms total)
37:
37: [----------] 10 tests from SurfaceAreaTest
37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (7 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (6 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints12
37: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints32
37: [ OK ] SurfaceAreaTest.SurfacePoints32 (3 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints42
37: [ OK ] SurfaceAreaTest.SurfacePoints42 (4 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints122
37: [ OK ] SurfaceAreaTest.SurfacePoints122 (7 ms)
37: [ RUN ] SurfaceAreaTest.Computes100Points
37: [ OK ] SurfaceAreaTest.Computes100Points (5 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (15 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (17 ms)
37: [----------] 10 tests from SurfaceAreaTest (70 ms total)
37:
37: [----------] 4 tests from TopologyInformation
37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
37: [ RUN ] TopologyInformation.WorksWithGroFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithGroFile (25 ms)
37: [ RUN ] TopologyInformation.WorksWithPdbFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithPdbFile (25 ms)
37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1879509571
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
37:
37: NOTE 2 [file lysozyme.top, line 1465]:
37: System has non-zero total charge: 2.000000
37: Total charge should normally be an integer. See
37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
37: for discussion on how close it should be to an integer.
37:
37:
37:
37: Number of degrees of freedom in T-Coupling group rest is 465.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
37: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
37: Analysing residue names:
37: There are: 10 Protein residues
37: Analysing Protein...
37: This run will generate roughly 0 Mb of data
37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (3795 ms)
37: [----------] 4 tests from TopologyInformation (3846 ms total)
37:
37: [----------] 4 tests from TrajectoryModuleTest
37: [ RUN ] TrajectoryModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.BasicTest (22 ms)
37: [ RUN ] TrajectoryModuleTest.PlotsXOnly
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.PlotsXOnly (22 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (20 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoForces
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoForces (20 ms)
37: [----------] 4 tests from TrajectoryModuleTest (85 ms total)
37:
37: [----------] 5 tests from UnionFinderTest
37: [ RUN ] UnionFinderTest.WorksEmpty
37: [ OK ] UnionFinderTest.WorksEmpty (0 ms)
37: [ RUN ] UnionFinderTest.BasicMerges
37: [ OK ] UnionFinderTest.BasicMerges (0 ms)
37: [ RUN ] UnionFinderTest.LargerMerges
37: [ OK ] UnionFinderTest.LargerMerges (1 ms)
37: [ RUN ] UnionFinderTest.LongRightMerge
37: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
37: [ RUN ] UnionFinderTest.LongLeftMerge
37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
37: [----------] 5 tests from UnionFinderTest (1 ms total)
37:
37: [----------] 1 test from MappedUnionFinderTest
37: [ RUN ] MappedUnionFinderTest.BasicMerges
37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
37: [----------] 1 test from MappedUnionFinderTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 82 tests from 16 test cases ran. (7671 ms total)
37: [ PASSED ] 82 tests.
37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 7.75 sec
test 38
Start 38: EnergyAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/EnergyAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 7 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 1 test from DhdlTest
38: [ RUN ] DhdlTest.ExtractDhdl
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
38: Note: file tpx version 110, software tpx version 119
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
38:
38:
38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
38: [ OK ] DhdlTest.ExtractDhdl (94 ms)
38: [----------] 1 test from DhdlTest (97 ms total)
38:
38: [----------] 1 test from OriresTest
38: [ RUN ] OriresTest.ExtractOrires
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
38: Note: file tpx version 111, software tpx version 119
38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
38: End your selection with 0
38: Selecting all 7 orientation restraints
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
38: [ OK ] OriresTest.ExtractOrires (82 ms)
38: [----------] 1 test from OriresTest (83 ms total)
38:
38: [----------] 3 tests from EnergyTest
38: [ RUN ] EnergyTest.ExtractEnergy
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: [ OK ] EnergyTest.ExtractEnergy (18 ms)
38: [ RUN ] EnergyTest.ExtractEnergyByNumber
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Pres. DC -268.49 3 8.52175 13.2804 (bar)
38: [ OK ] EnergyTest.ExtractEnergyByNumber (16 ms)
38: [ RUN ] EnergyTest.ExtractEnergyMixed
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: [ OK ] EnergyTest.ExtractEnergyMixed (17 ms)
38: [----------] 3 tests from EnergyTest (53 ms total)
38:
38: [----------] 2 tests from ViscosityTest
38: [ RUN ] ViscosityTest.EinsteinViscosity
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosity (83 ms)
38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (82 ms)
38: [----------] 2 tests from ViscosityTest (167 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 7 tests from 4 test cases ran. (400 ms total)
38: [ PASSED ] 7 tests.
38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 0.47 sec
test 39
Start 39: ToolUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/ToolUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 18 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from DumpTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -1292018722
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] DumpTest.WorksWithTpr
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
39: /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
39: inputrec:
39: integrator = md
39: tinit = 0
39: dt = 0.001
39: nsteps = 0
39: init-step = 0
39: simulation-part = 1
39: comm-mode = Linear
39: nstcomm = 100
39: bd-fric = 0
39: ld-seed = -1292018722
39: emtol = 10
39: emstep = 0.01
39: niter = 20
39: fcstep = 0
39: nstcgsteep = 1000
39: nbfgscorr = 10
39: rtpi = 0.05
39: nstxout = 0
39: nstvout = 0
39: nstfout = 0
39: nstlog = 1000
39: nstcalcenergy = 100
39: nstenergy = 1000
39: nstxout-compressed = 0
39: compressed-x-precision = 1000
39: cutoff-scheme = Verlet
39: nstlist = 10
39: pbc = xyz
39: periodic-molecules = false
39: verlet-buffer-tolerance = -1
39: rlist = 1.1
39: coulombtype = Cut-off
39: coulomb-modifier = Potential-shift
39: rcoulomb-switch = 0
39: rcoulomb = 1
39: epsilon-r = 1
39: epsilon-rf = inf
39: vdw-type = Cut-off
39: vdw-modifier = Potential-shift
39: rvdw-switch = 0
39: rvdw = 1
39: DispCorr = No
39: table-extension = 1
39: fourierspacing = 0.12
39: fourier-nx = 0
39: fourier-ny = 0
39: fourier-nz = 0
39: pme-order = 4
39: ewald-rtol = 1e-05
39: ewald-rtol-lj = 0.001
39: lj-pme-comb-rule = Geometric
39: ewald-geometry = 0
39: epsilon-surface = 0
39: tcoupl = No
39: nsttcouple = -1
39: nh-chain-length = 0
39: print-nose-hoover-chain-variables = false
39: pcoupl = No
39: pcoupltype = Isotropic
39: nstpcouple = -1
39: tau-p = 1
39: compressibility (3x3):
39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p (3x3):
39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: refcoord-scaling = No
39: posres-com (3):
39: posres-com[0]= 0.00000e+00
39: posres-com[1]= 0.00000e+00
39: posres-com[2]= 0.00000e+00
39: posres-comB (3):
39: posres-comB[0]= 0.00000e+00
39: posres-comB[1]= 0.00000e+00
39: posres-comB[2]= 0.00000e+00
39: QMMM = false
39: QMconstraints = 0
39: QMMMscheme = 0
39: MMChargeScaleFactor = 1
39: qm-opts:
39: ngQM = 0
39: constraint-algorithm = Lincs
39: continuation = false
39: Shake-SOR = false
39: shake-tol = 0.0001
39: lincs-order = 4
39: lincs-iter = 1
39: lincs-warnangle = 30
39: nwall = 0
39: wall-type = 9-3
39: wall-r-linpot = -1
39: wall-atomtype[0] = -1
39: wall-atomtype[1] = -1
39: wall-density[0] = 0
39: wall-density[1] = 0
39: wall-ewald-zfac = 3
39: pull = false
39: awh = false
39: rotation = false
39: interactiveMD = false
39: disre = No
39: disre-weighting = Conservative
39: disre-mixed = false
39: dr-fc = 1000
39: dr-tau = 0
39: nstdisreout = 100
39: orire-fc = 0
39: orire-tau = 0
39: nstorireout = 100
39: free-energy = no
39: cos-acceleration = 0
39: deform (3x3):
39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: simulated-tempering = false
39: swapcoords = no
39: userint1 = 0
39: userint2 = 0
39: userint3 = 0
39: userint4 = 0
39: userreal1 = 0
39: userreal2 = 0
39: userreal3 = 0
39: userreal4 = 0
39: applied-forces:
39: electric-field:
39: x:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: y:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: z:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: density-guided-simulation:
39: active = false
39: group = protein
39: similarity-measure = inner-product
39: atom-spreading-weight = unity
39: force-constant = 1e+09
39: gaussian-transform-spreading-width = 0.2
39: gaussian-transform-spreading-range-in-multiples-of-width = 4
39: reference-density-filename = reference.mrc
39: nst = 1
39: normalize-densities = true
39: adaptive-force-scaling = false
39: adaptive-force-scaling-time-constant = 4
39: grpopts:
39: nrdf: 465
39: ref-t: 0
39: tau-t: 0
39: annealing: No
39: annealing-npoints: 0
39: acc: 0 0 0
39: nfreeze: N N N
39: energygrp-flags[ 0]: 0
39: header:
39: bIr = present
39: bBox = present
39: bTop = present
39: bX = present
39: bV = present
39: bF = not present
39: natoms = 156
39: lambda = 0.000000e+00
39: buffer size = 59422
39: topology:
39: name="First 10 residues from 1AKI"
39: #atoms = 156
39: #molblock = 1
39: molblock (0):
39: moltype = 0 "Protein_chain_B"
39: #molecules = 1
39: #posres_xA = 0
39: #posres_xB = 0
39: bIntermolecularInteractions = false
39: ffparams:
39: atnr=10
39: ntypes=212
39: functype[0]=LJ_SR, c6= 3.35274590e-03, c12= 3.95094276e-06
39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[2]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
39: functype[3]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
39: functype[4]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
39: functype[5]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
39: functype[6]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
39: functype[7]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
39: functype[8]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
39: functype[9]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[20]=LJ_SR, c6= 2.60916958e-03, c12= 3.84022405e-06
39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[22]=LJ_SR, c6= 2.03050394e-03, c12= 3.73260514e-06
39: functype[23]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
39: functype[24]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
39: functype[25]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
39: functype[26]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
39: functype[27]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
39: functype[28]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
39: functype[29]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
39: functype[30]=LJ_SR, c6= 6.41072227e-04, c12= 3.43856414e-07
39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[32]=LJ_SR, c6= 4.98894195e-04, c12= 3.34220175e-07
39: functype[33]=LJ_SR, c6= 1.22578131e-04, c12= 2.99263014e-08
39: functype[34]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
39: functype[35]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
39: functype[36]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
39: functype[37]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
39: functype[38]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
39: functype[39]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
39: functype[40]=LJ_SR, c6= 4.04775795e-03, c12= 7.32754188e-06
39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[42]=LJ_SR, c6= 3.15004122e-03, c12= 7.12220026e-06
39: functype[43]=LJ_SR, c6= 7.73964217e-04, c12= 6.37726998e-07
39: functype[44]=LJ_SR, c6= 4.88684513e-03, c12= 1.35898972e-05
39: functype[45]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
39: functype[46]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
39: functype[47]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
39: functype[48]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
39: functype[49]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
39: functype[50]=LJ_SR, c6= 2.81521026e-03, c12= 2.50631660e-06
39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[52]=LJ_SR, c6= 2.19085021e-03, c12= 2.43608270e-06
39: functype[53]=LJ_SR, c6= 5.38290828e-04, c12= 2.18128321e-07
39: functype[54]=LJ_SR, c6= 3.39879468e-03, c12= 4.64829736e-06
39: functype[55]=LJ_SR, c6= 2.36385735e-03, c12= 1.58990645e-06
39: functype[56]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
39: functype[57]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
39: functype[58]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
39: functype[59]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
39: functype[60]=LJ_SR, c6= 2.80388421e-03, c12= 4.30620821e-06
39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[62]=LJ_SR, c6= 2.18203571e-03, c12= 4.18553600e-06
39: functype[63]=LJ_SR, c6= 5.36125386e-04, c12= 3.74775709e-07
39: functype[64]=LJ_SR, c6= 3.38512054e-03, c12= 7.98643487e-06
39: functype[65]=LJ_SR, c6= 2.35434738e-03, c12= 2.73168575e-06
39: functype[66]=LJ_SR, c6= 2.34487536e-03, c12= 4.69342376e-06
39: functype[67]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
39: functype[68]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
39: functype[69]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
39: functype[70]=LJ_SR, c6= 5.81477652e-04, c12= 2.82897616e-07
39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[72]=LJ_SR, c6= 4.52516542e-04, c12= 2.74969580e-07
39: functype[73]=LJ_SR, c6= 1.11183173e-04, c12= 2.46209719e-08
39: functype[74]=LJ_SR, c6= 7.02015939e-04, c12= 5.24670895e-07
39: functype[75]=LJ_SR, c6= 4.88250953e-04, c12= 1.79458596e-07
39: functype[76]=LJ_SR, c6= 4.86286852e-04, c12= 3.08335643e-07
39: functype[77]=LJ_SR, c6= 1.00847494e-04, c12= 2.02561683e-08
39: functype[78]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
39: functype[79]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
39: functype[80]=LJ_SR, c6= 6.03335386e-04, c12= 2.35915493e-07
39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[82]=LJ_SR, c6= 4.69526683e-04, c12= 2.29304163e-07
39: functype[83]=LJ_SR, c6= 1.15362534e-04, c12= 2.05320472e-08
39: functype[84]=LJ_SR, c6= 7.28404266e-04, c12= 4.37535846e-07
39: functype[85]=LJ_SR, c6= 5.06604381e-04, c12= 1.49655136e-07
39: functype[86]=LJ_SR, c6= 5.04566357e-04, c12= 2.57128875e-07
39: functype[87]=LJ_SR, c6= 1.04638377e-04, c12= 1.68921392e-08
39: functype[88]=LJ_SR, c6= 1.08571716e-04, c12= 1.40867806e-08
39: functype[89]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
39: functype[90]=LJ_SR, c6= 7.20490469e-03, c12= 1.15394714e-05
39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[92]=LJ_SR, c6= 5.60698984e-03, c12= 1.12160897e-05
39: functype[93]=LJ_SR, c6= 1.37763575e-03, c12= 1.00429668e-06
39: functype[94]=LJ_SR, c6= 8.69845692e-03, c12= 2.14014708e-05
39: functype[95]=LJ_SR, c6= 6.04976481e-03, c12= 7.32016997e-06
39: functype[96]=LJ_SR, c6= 6.02542516e-03, c12= 1.25770912e-05
39: functype[97]=LJ_SR, c6= 1.24956947e-03, c12= 8.26254961e-07
39: functype[98]=LJ_SR, c6= 1.29654107e-03, c12= 6.89035176e-07
39: functype[99]=LJ_SR, c6= 1.54830217e-02, c12= 3.37031743e-05
39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39319992e+01, phiB= 1.80000000e+02, cpB= 4.39319992e+01, mult=2
39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400002e+00, phiB= 1.80000000e+02, cpB= 4.18400002e+00, mult=2
39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60239983e+00, phiB= 1.80000000e+02, cpB= 4.60239983e+00, mult=2
39: functype[143]=RBDIHS, rbcA[0]= 5.46010017e-01, rbcA[1]= 1.63803005e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405008e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.46010017e-01, rbcB[1]= 1.63803005e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405008e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[144]=RBDIHS, rbcA[0]= 7.25920022e-01, rbcA[1]= 2.17776990e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 7.25920022e-01, rbcB[1]= 2.17776990e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[145]=RBDIHS, rbcA[0]= 1.27611995e+00, rbcA[1]= 1.16734004e+00, rbcA[2]= 8.95380020e-01, rbcA[3]=-3.33884001e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.27611995e+00, rbcB[1]= 1.16734004e+00, rbcB[2]= 8.95380020e-01, rbcB[3]=-3.33884001e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[146]=RBDIHS, rbcA[0]=-6.91824007e+00, rbcA[1]= 4.67562008e+00, rbcA[2]= 2.24261999e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-6.91824007e+00, rbcB[1]= 4.67562008e+00, rbcB[2]= 2.24261999e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[147]=RBDIHS, rbcA[0]= 9.70690012e-01, rbcA[1]= 2.91206002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275003e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.70690012e-01, rbcB[1]= 2.91206002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275003e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[148]=RBDIHS, rbcA[0]= 6.27600014e-01, rbcA[1]= 1.88279998e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040006e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 6.27600014e-01, rbcB[1]= 1.88279998e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040006e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[149]=RBDIHS, rbcA[0]=-1.58989996e-01, rbcA[1]=-4.76980001e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35959983e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.58989996e-01, rbcB[1]=-4.76980001e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35959983e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654020e+00, rbcA[2]=-1.04934702e+01, rbcA[3]= 6.73623991e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654020e+00, rbcB[2]=-1.04934702e+01, rbcB[3]= 6.73623991e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[151]=RBDIHS, rbcA[0]= 5.00825024e+00, rbcA[1]=-1.69869995e+00, rbcA[2]=-3.72379988e-01, rbcA[3]=-2.93716002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.00825024e+00, rbcB[1]=-1.69869995e+00, rbcB[2]=-3.72379988e-01, rbcB[3]=-2.93716002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[152]=RBDIHS, rbcA[0]= 2.92880011e+00, rbcA[1]=-1.46440005e+00, rbcA[2]= 2.09199995e-01, rbcA[3]=-1.67359996e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.92880011e+00, rbcB[1]=-1.46440005e+00, rbcB[2]= 2.09199995e-01, rbcB[3]=-1.67359996e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[153]=RBDIHS, rbcA[0]= 5.77183008e+00, rbcA[1]=-2.67147994e+00, rbcA[2]= 9.58140016e-01, rbcA[3]=-4.05847979e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.77183008e+00, rbcB[1]=-2.67147994e+00, rbcB[2]= 9.58140016e-01, rbcB[3]=-4.05847979e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[154]=RBDIHS, rbcA[0]= 8.03330004e-01, rbcA[1]= 2.40999007e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.03330004e-01, rbcB[1]= 2.40999007e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[155]=RBDIHS, rbcA[0]= 2.05016003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.05016003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[156]=RBDIHS, rbcA[0]= 3.02879791e+01, rbcA[1]=-4.81160021e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.02879791e+01, rbcB[1]=-4.81160021e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[157]=RBDIHS, rbcA[0]= 2.54763794e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763794e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.54763794e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763794e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[158]=RBDIHS, rbcA[0]= 1.57025499e+01, rbcA[1]= 3.17565594e+01, rbcA[2]=-3.66935992e+00, rbcA[3]=-4.37897491e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.57025499e+01, rbcB[1]= 3.17565594e+01, rbcB[2]=-3.66935992e+00, rbcB[3]=-4.37897491e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[159]=RBDIHS, rbcA[0]=-1.03574896e+01, rbcA[1]=-2.95871601e+01, rbcA[2]=-1.16734004e+00, rbcA[3]= 4.11119919e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.03574896e+01, rbcB[1]=-2.95871601e+01, rbcB[2]=-1.16734004e+00, rbcB[3]= 4.11119919e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[160]=RBDIHS, rbcA[0]= 4.50198984e+00, rbcA[1]= 7.82410026e-01, rbcA[2]=-1.60247004e+00, rbcA[3]=-3.68192005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.50198984e+00, rbcB[1]= 7.82410026e-01, rbcB[2]=-1.60247004e+00, rbcB[3]=-3.68192005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[161]=RBDIHS, rbcA[0]= 4.22589988e-01, rbcA[1]= 2.70705009e+00, rbcA[2]=-3.12964010e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.22589988e-01, rbcB[1]= 2.70705009e+00, rbcB[2]=-3.12964010e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[162]=RBDIHS, rbcA[0]=-7.65670002e-01, rbcA[1]= 2.70705009e+00, rbcA[2]= 4.02501011e+00, rbcA[3]=-5.96639013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-7.65670002e-01, rbcB[1]= 2.70705009e+00, rbcB[2]= 4.02501011e+00, rbcB[3]=-5.96639013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[163]=RBDIHS, rbcA[0]= 9.66499984e-01, rbcA[1]= 2.89950991e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86600995e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.66499984e-01, rbcB[1]= 2.89950991e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86600995e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[164]=RBDIHS, rbcA[0]=-4.23421001e+00, rbcA[1]= 7.22159004e+00, rbcA[2]= 1.90789998e+00, rbcA[3]=-4.89527988e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.23421001e+00, rbcB[1]= 7.22159004e+00, rbcB[2]= 1.90789998e+00, rbcB[3]=-4.89527988e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[165]=RBDIHS, rbcA[0]= 3.03339996e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03339996e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.03339996e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03339996e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[166]=RBDIHS, rbcA[0]= 1.02319698e+01, rbcA[1]= 3.52082992e+00, rbcA[2]=-3.97899008e+00, rbcA[3]=-9.77381992e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.02319698e+01, rbcB[1]= 3.52082992e+00, rbcB[2]=-3.97899008e+00, rbcB[3]=-9.77381992e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[167]=RBDIHS, rbcA[0]= 5.49777985e+00, rbcA[1]= 1.41838002e+00, rbcA[2]=-6.91615009e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.49777985e+00, rbcB[1]= 1.41838002e+00, rbcB[2]=-6.91615009e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[168]=RBDIHS, rbcA[0]=-1.21755004e+00, rbcA[1]=-3.65264010e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018013e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.21755004e+00, rbcB[1]=-3.65264010e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018013e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[169]=RBDIHS, rbcA[0]=-1.26775002e+00, rbcA[1]= 3.02084994e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49781990e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.26775002e+00, rbcB[1]= 3.02084994e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49781990e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[170]=RBDIHS, rbcA[0]= 3.80117011e+00, rbcA[1]=-6.95172024e+00, rbcA[2]=-1.01671004e+00, rbcA[3]= 4.16726017e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.80117011e+00, rbcB[1]=-6.95172024e+00, rbcB[2]=-1.01671004e+00, rbcB[3]= 4.16726017e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[171]=RBDIHS, rbcA[0]= 3.70279998e-01, rbcA[1]= 1.11085999e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.70279998e-01, rbcB[1]= 1.11085999e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[172]=RBDIHS, rbcA[0]= 3.32042198e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042198e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.32042198e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042198e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[173]=RBDIHS, rbcA[0]= 1.63176003e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176003e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.63176003e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176003e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[174]=RBDIHS, rbcA[0]= 3.40787005e+00, rbcA[1]=-2.80537009e+00, rbcA[2]=-3.59820008e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.40787005e+00, rbcB[1]=-2.80537009e+00, rbcB[2]=-3.59820008e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[175]=RBDIHS, rbcA[0]=-1.62590199e+01, rbcA[1]= 9.08765030e+00, rbcA[2]= 7.17138004e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.62590199e+01, rbcB[1]= 9.08765030e+00, rbcB[2]= 7.17138004e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[176]=RBDIHS, rbcA[0]= 9.45590019e-01, rbcA[1]= 2.83675003e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234005e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.45590019e-01, rbcB[1]= 2.83675003e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234005e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[177]=RBDIHS, rbcA[0]=-1.50624001e+00, rbcA[1]= 5.37225008e+00, rbcA[2]= 1.17989004e+00, rbcA[3]=-5.04589987e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.50624001e+00, rbcB[1]= 5.37225008e+00, rbcB[2]= 1.17989004e+00, rbcB[3]=-5.04589987e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[178]=RBDIHS, rbcA[0]= 1.00416005e+00, rbcA[1]= 3.01248002e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664019e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.00416005e+00, rbcB[1]= 3.01248002e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664019e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[179]=RBDIHS, rbcA[0]= 8.79267979e+00, rbcA[1]=-1.18344402e+01, rbcA[2]= 1.07528996e+00, rbcA[3]= 1.96648002e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.79267979e+00, rbcB[1]=-1.18344402e+01, rbcB[2]= 1.07528996e+00, rbcB[3]= 1.96648002e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[180]=RBDIHS, rbcA[0]=-5.77392006e+00, rbcA[1]= 3.38485003e+00, rbcA[2]= 2.38906002e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-5.77392006e+00, rbcB[1]= 3.38485003e+00, rbcB[2]= 2.38906002e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[181]=RBDIHS, rbcA[0]=-9.08345985e+00, rbcA[1]= 9.75708961e+00, rbcA[2]= 3.45180011e+00, rbcA[3]=-4.12542009e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-9.08345985e+00, rbcB[1]= 9.75708961e+00, rbcB[2]= 3.45180011e+00, rbcB[3]=-4.12542009e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[182]=RBDIHS, rbcA[0]=-4.70699996e-01, rbcA[1]=-1.41209996e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88279998e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.70699996e-01, rbcB[1]=-1.41209996e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88279998e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[183]=RBDIHS, rbcA[0]= 3.43088007e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088007e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.43088007e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088007e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[184]=RBDIHS, rbcA[0]= 2.57315993e+00, rbcA[1]= 3.49781990e+00, rbcA[2]=-1.10038996e+00, rbcA[3]=-4.97059011e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.57315993e+00, rbcB[1]= 3.49781990e+00, rbcB[2]=-1.10038996e+00, rbcB[3]=-4.97059011e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[185]=RBDIHS, rbcA[0]=-8.22160006e-01, rbcA[1]= 1.12758994e+00, rbcA[2]=-3.05440009e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-8.22160006e-01, rbcB[1]= 1.12758994e+00, rbcB[2]=-3.05440009e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[186]=LJ14, c6A= 3.20536114e-04, c12A= 1.71928207e-07, c6B= 3.20536114e-04, c12B= 1.71928207e-07
39: functype[187]=LJ14, c6A= 1.30458479e-03, c12A= 1.92011203e-06, c6B= 1.30458479e-03, c12B= 1.92011203e-06
39: functype[188]=LJ14, c6A= 1.40760513e-03, c12A= 1.25315830e-06, c6B= 1.40760513e-03, c12B= 1.25315830e-06
39: functype[189]=LJ14, c6A= 1.67637295e-03, c12A= 1.97547138e-06, c6B= 1.67637295e-03, c12B= 1.97547138e-06
39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
39: functype[191]=LJ14, c6A= 2.49447097e-04, c12A= 1.67110088e-07, c6B= 2.49447097e-04, c12B= 1.67110088e-07
39: functype[192]=LJ14, c6A= 1.01525197e-03, c12A= 1.86630257e-06, c6B= 1.01525197e-03, c12B= 1.86630257e-06
39: functype[193]=LJ14, c6A= 6.12890653e-05, c12A= 1.49631507e-08, c6B= 6.12890653e-05, c12B= 1.49631507e-08
39: functype[194]=LJ14, c6A= 2.69145414e-04, c12A= 1.09064160e-07, c6B= 2.69145414e-04, c12B= 1.09064160e-07
39: functype[195]=LJ14, c6A= 1.09542510e-03, c12A= 1.21804135e-06, c6B= 1.09542510e-03, c12B= 1.21804135e-06
39: functype[196]=LJ14, c6A= 3.86982108e-04, c12A= 3.18863499e-07, c6B= 3.86982108e-04, c12B= 3.18863499e-07
39: functype[197]=LJ14, c6A= 1.57502061e-03, c12A= 3.56110013e-06, c6B= 1.57502061e-03, c12B= 3.56110013e-06
39: functype[198]=LJ14, c6A= 2.44342256e-03, c12A= 6.79494860e-06, c6B= 2.44342256e-03, c12B= 6.79494860e-06
39: functype[199]=LJ14, c6A= 1.40194211e-03, c12A= 2.15310411e-06, c6B= 1.40194211e-03, c12B= 2.15310411e-06
39: functype[200]=LJ14, c6A= 1.09101785e-03, c12A= 2.09276800e-06, c6B= 1.09101785e-03, c12B= 2.09276800e-06
39: functype[201]=LJ14, c6A= 2.68062693e-04, c12A= 1.87387855e-07, c6B= 2.68062693e-04, c12B= 1.87387855e-07
39: functype[202]=LJ14, c6A= 2.26258271e-04, c12A= 1.37484790e-07, c6B= 2.26258271e-04, c12B= 1.37484790e-07
39: functype[203]=LJ14, c6A= 2.43143426e-04, c12A= 1.54167822e-07, c6B= 2.43143426e-04, c12B= 1.54167822e-07
39: functype[204]=LJ14, c6A= 1.17243768e-03, c12A= 2.34671188e-06, c6B= 1.17243768e-03, c12B= 2.34671188e-06
39: functype[205]=LJ14, c6A= 1.69256027e-03, c12A= 3.99321743e-06, c6B= 1.69256027e-03, c12B= 3.99321743e-06
39: functype[206]=LJ14, c6A= 5.04237469e-05, c12A= 1.01280841e-08, c6B= 5.04237469e-05, c12B= 1.01280841e-08
39: functype[207]=LJ14, c6A= 2.34763342e-04, c12A= 1.14652082e-07, c6B= 2.34763342e-04, c12B= 1.14652082e-07
39: functype[208]=LJ14, c6A= 5.76812672e-05, c12A= 1.02660236e-08, c6B= 5.76812672e-05, c12B= 1.02660236e-08
39: functype[209]=LJ14, c6A= 3.60245234e-03, c12A= 5.76973571e-06, c6B= 3.60245234e-03, c12B= 5.76973571e-06
39: functype[210]=LJ14, c6A= 6.88817876e-04, c12A= 5.02148339e-07, c6B= 6.88817876e-04, c12B= 5.02148339e-07
39: functype[211]=LJ14, c6A= 4.34922846e-03, c12A= 1.07007354e-05, c6B= 4.34922846e-03, c12B= 1.07007354e-05
39: reppow = 12
39: fudgeQQ = 0.5
39: cmap
39: atomtypes:
39: atomtype[ 0]={atomnumber= 7}
39: atomtype[ 1]={atomnumber= 1}
39: atomtype[ 2]={atomnumber= 6}
39: atomtype[ 3]={atomnumber= 1}
39: atomtype[ 4]={atomnumber= 6}
39: atomtype[ 5]={atomnumber= 8}
39: atomtype[ 6]={atomnumber= 6}
39: atomtype[ 7]={atomnumber= 1}
39: atomtype[ 8]={atomnumber= 6}
39: atomtype[ 9]={atomnumber= 16}
39: moltype (0):
39: name="Protein_chain_B"
39: atoms:
39: atom (156):
39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
39: atom (156):
39: atom[0]={name="N"}
39: atom[1]={name="H1"}
39: atom[2]={name="H2"}
39: atom[3]={name="H3"}
39: atom[4]={name="CA"}
39: atom[5]={name="HA"}
39: atom[6]={name="CB"}
39: atom[7]={name="HB1"}
39: atom[8]={name="HB2"}
39: atom[9]={name="CG"}
39: atom[10]={name="HG1"}
39: atom[11]={name="HG2"}
39: atom[12]={name="CD"}
39: atom[13]={name="HD1"}
39: atom[14]={name="HD2"}
39: atom[15]={name="CE"}
39: atom[16]={name="HE1"}
39: atom[17]={name="HE2"}
39: atom[18]={name="NZ"}
39: atom[19]={name="HZ1"}
39: atom[20]={name="HZ2"}
39: atom[21]={name="HZ3"}
39: atom[22]={name="C"}
39: atom[23]={name="O"}
39: atom[24]={name="N"}
39: atom[25]={name="H"}
39: atom[26]={name="CA"}
39: atom[27]={name="HA"}
39: atom[28]={name="CB"}
39: atom[29]={name="HB"}
39: atom[30]={name="CG1"}
39: atom[31]={name="HG11"}
39: atom[32]={name="HG12"}
39: atom[33]={name="HG13"}
39: atom[34]={name="CG2"}
39: atom[35]={name="HG21"}
39: atom[36]={name="HG22"}
39: atom[37]={name="HG23"}
39: atom[38]={name="C"}
39: atom[39]={name="O"}
39: atom[40]={name="N"}
39: atom[41]={name="H"}
39: atom[42]={name="CA"}
39: atom[43]={name="HA"}
39: atom[44]={name="CB"}
39: atom[45]={name="HB1"}
39: atom[46]={name="HB2"}
39: atom[47]={name="CG"}
39: atom[48]={name="CD1"}
39: atom[49]={name="HD1"}
39: atom[50]={name="CD2"}
39: atom[51]={name="HD2"}
39: atom[52]={name="CE1"}
39: atom[53]={name="HE1"}
39: atom[54]={name="CE2"}
39: atom[55]={name="HE2"}
39: atom[56]={name="CZ"}
39: atom[57]={name="HZ"}
39: atom[58]={name="C"}
39: atom[59]={name="O"}
39: atom[60]={name="N"}
39: atom[61]={name="H"}
39: atom[62]={name="CA"}
39: atom[63]={name="HA1"}
39: atom[64]={name="HA2"}
39: atom[65]={name="C"}
39: atom[66]={name="O"}
39: atom[67]={name="N"}
39: atom[68]={name="H"}
39: atom[69]={name="CA"}
39: atom[70]={name="HA"}
39: atom[71]={name="CB"}
39: atom[72]={name="HB1"}
39: atom[73]={name="HB2"}
39: atom[74]={name="CG"}
39: atom[75]={name="HG1"}
39: atom[76]={name="HG2"}
39: atom[77]={name="CD"}
39: atom[78]={name="HD1"}
39: atom[79]={name="HD2"}
39: atom[80]={name="NE"}
39: atom[81]={name="HE"}
39: atom[82]={name="CZ"}
39: atom[83]={name="NH1"}
39: atom[84]={name="HH11"}
39: atom[85]={name="HH12"}
39: atom[86]={name="NH2"}
39: atom[87]={name="HH21"}
39: atom[88]={name="HH22"}
39: atom[89]={name="C"}
39: atom[90]={name="O"}
39: atom[91]={name="N"}
39: atom[92]={name="H"}
39: atom[93]={name="CA"}
39: atom[94]={name="HA"}
39: atom[95]={name="CB"}
39: atom[96]={name="HB1"}
39: atom[97]={name="HB2"}
39: atom[98]={name="SG"}
39: atom[99]={name="HG"}
39: atom[100]={name="C"}
39: atom[101]={name="O"}
39: atom[102]={name="N"}
39: atom[103]={name="H"}
39: atom[104]={name="CA"}
39: atom[105]={name="HA"}
39: atom[106]={name="CB"}
39: atom[107]={name="HB1"}
39: atom[108]={name="HB2"}
39: atom[109]={name="CG"}
39: atom[110]={name="HG1"}
39: atom[111]={name="HG2"}
39: atom[112]={name="CD"}
39: atom[113]={name="OE1"}
39: atom[114]={name="OE2"}
39: atom[115]={name="C"}
39: atom[116]={name="O"}
39: atom[117]={name="N"}
39: atom[118]={name="H"}
39: atom[119]={name="CA"}
39: atom[120]={name="HA"}
39: atom[121]={name="CB"}
39: atom[122]={name="HB1"}
39: atom[123]={name="HB2"}
39: atom[124]={name="CG"}
39: atom[125]={name="HG"}
39: atom[126]={name="CD1"}
39: atom[127]={name="HD11"}
39: atom[128]={name="HD12"}
39: atom[129]={name="HD13"}
39: atom[130]={name="CD2"}
39: atom[131]={name="HD21"}
39: atom[132]={name="HD22"}
39: atom[133]={name="HD23"}
39: atom[134]={name="C"}
39: atom[135]={name="O"}
39: atom[136]={name="N"}
39: atom[137]={name="H"}
39: atom[138]={name="CA"}
39: atom[139]={name="HA"}
39: atom[140]={name="CB"}
39: atom[141]={name="HB1"}
39: atom[142]={name="HB2"}
39: atom[143]={name="HB3"}
39: atom[144]={name="C"}
39: atom[145]={name="O"}
39: atom[146]={name="N"}
39: atom[147]={name="H"}
39: atom[148]={name="CA"}
39: atom[149]={name="HA"}
39: atom[150]={name="CB"}
39: atom[151]={name="HB1"}
39: atom[152]={name="HB2"}
39: atom[153]={name="HB3"}
39: atom[154]={name="C"}
39: atom[155]={name="O"}
39: type (156):
39: type[0]={name="opls_287",nameB="opls_287"}
39: type[1]={name="opls_290",nameB="opls_290"}
39: type[2]={name="opls_290",nameB="opls_290"}
39: type[3]={name="opls_290",nameB="opls_290"}
39: type[4]={name="opls_293B",nameB="opls_293B"}
39: type[5]={name="opls_140",nameB="opls_140"}
39: type[6]={name="opls_136",nameB="opls_136"}
39: type[7]={name="opls_140",nameB="opls_140"}
39: type[8]={name="opls_140",nameB="opls_140"}
39: type[9]={name="opls_136",nameB="opls_136"}
39: type[10]={name="opls_140",nameB="opls_140"}
39: type[11]={name="opls_140",nameB="opls_140"}
39: type[12]={name="opls_136",nameB="opls_136"}
39: type[13]={name="opls_140",nameB="opls_140"}
39: type[14]={name="opls_140",nameB="opls_140"}
39: type[15]={name="opls_292",nameB="opls_292"}
39: type[16]={name="opls_140",nameB="opls_140"}
39: type[17]={name="opls_140",nameB="opls_140"}
39: type[18]={name="opls_287",nameB="opls_287"}
39: type[19]={name="opls_290",nameB="opls_290"}
39: type[20]={name="opls_290",nameB="opls_290"}
39: type[21]={name="opls_290",nameB="opls_290"}
39: type[22]={name="opls_235",nameB="opls_235"}
39: type[23]={name="opls_236",nameB="opls_236"}
39: type[24]={name="opls_238",nameB="opls_238"}
39: type[25]={name="opls_241",nameB="opls_241"}
39: type[26]={name="opls_224B",nameB="opls_224B"}
39: type[27]={name="opls_140",nameB="opls_140"}
39: type[28]={name="opls_137",nameB="opls_137"}
39: type[29]={name="opls_140",nameB="opls_140"}
39: type[30]={name="opls_135",nameB="opls_135"}
39: type[31]={name="opls_140",nameB="opls_140"}
39: type[32]={name="opls_140",nameB="opls_140"}
39: type[33]={name="opls_140",nameB="opls_140"}
39: type[34]={name="opls_135",nameB="opls_135"}
39: type[35]={name="opls_140",nameB="opls_140"}
39: type[36]={name="opls_140",nameB="opls_140"}
39: type[37]={name="opls_140",nameB="opls_140"}
39: type[38]={name="opls_235",nameB="opls_235"}
39: type[39]={name="opls_236",nameB="opls_236"}
39: type[40]={name="opls_238",nameB="opls_238"}
39: type[41]={name="opls_241",nameB="opls_241"}
39: type[42]={name="opls_224B",nameB="opls_224B"}
39: type[43]={name="opls_140",nameB="opls_140"}
39: type[44]={name="opls_149",nameB="opls_149"}
39: type[45]={name="opls_140",nameB="opls_140"}
39: type[46]={name="opls_140",nameB="opls_140"}
39: type[47]={name="opls_145",nameB="opls_145"}
39: type[48]={name="opls_145",nameB="opls_145"}
39: type[49]={name="opls_146",nameB="opls_146"}
39: type[50]={name="opls_145",nameB="opls_145"}
39: type[51]={name="opls_146",nameB="opls_146"}
39: type[52]={name="opls_145",nameB="opls_145"}
39: type[53]={name="opls_146",nameB="opls_146"}
39: type[54]={name="opls_145",nameB="opls_145"}
39: type[55]={name="opls_146",nameB="opls_146"}
39: type[56]={name="opls_145",nameB="opls_145"}
39: type[57]={name="opls_146",nameB="opls_146"}
39: type[58]={name="opls_235",nameB="opls_235"}
39: type[59]={name="opls_236",nameB="opls_236"}
39: type[60]={name="opls_238",nameB="opls_238"}
39: type[61]={name="opls_241",nameB="opls_241"}
39: type[62]={name="opls_223B",nameB="opls_223B"}
39: type[63]={name="opls_140",nameB="opls_140"}
39: type[64]={name="opls_140",nameB="opls_140"}
39: type[65]={name="opls_235",nameB="opls_235"}
39: type[66]={name="opls_236",nameB="opls_236"}
39: type[67]={name="opls_238",nameB="opls_238"}
39: type[68]={name="opls_241",nameB="opls_241"}
39: type[69]={name="opls_224B",nameB="opls_224B"}
39: type[70]={name="opls_140",nameB="opls_140"}
39: type[71]={name="opls_136",nameB="opls_136"}
39: type[72]={name="opls_140",nameB="opls_140"}
39: type[73]={name="opls_140",nameB="opls_140"}
39: type[74]={name="opls_308",nameB="opls_308"}
39: type[75]={name="opls_140",nameB="opls_140"}
39: type[76]={name="opls_140",nameB="opls_140"}
39: type[77]={name="opls_307",nameB="opls_307"}
39: type[78]={name="opls_140",nameB="opls_140"}
39: type[79]={name="opls_140",nameB="opls_140"}
39: type[80]={name="opls_303",nameB="opls_303"}
39: type[81]={name="opls_304",nameB="opls_304"}
39: type[82]={name="opls_302",nameB="opls_302"}
39: type[83]={name="opls_300",nameB="opls_300"}
39: type[84]={name="opls_301",nameB="opls_301"}
39: type[85]={name="opls_301",nameB="opls_301"}
39: type[86]={name="opls_300",nameB="opls_300"}
39: type[87]={name="opls_301",nameB="opls_301"}
39: type[88]={name="opls_301",nameB="opls_301"}
39: type[89]={name="opls_235",nameB="opls_235"}
39: type[90]={name="opls_236",nameB="opls_236"}
39: type[91]={name="opls_238",nameB="opls_238"}
39: type[92]={name="opls_241",nameB="opls_241"}
39: type[93]={name="opls_224B",nameB="opls_224B"}
39: type[94]={name="opls_140",nameB="opls_140"}
39: type[95]={name="opls_206",nameB="opls_206"}
39: type[96]={name="opls_140",nameB="opls_140"}
39: type[97]={name="opls_140",nameB="opls_140"}
39: type[98]={name="opls_200",nameB="opls_200"}
39: type[99]={name="opls_204",nameB="opls_204"}
39: type[100]={name="opls_235",nameB="opls_235"}
39: type[101]={name="opls_236",nameB="opls_236"}
39: type[102]={name="opls_238",nameB="opls_238"}
39: type[103]={name="opls_241",nameB="opls_241"}
39: type[104]={name="opls_224B",nameB="opls_224B"}
39: type[105]={name="opls_140",nameB="opls_140"}
39: type[106]={name="opls_136",nameB="opls_136"}
39: type[107]={name="opls_140",nameB="opls_140"}
39: type[108]={name="opls_140",nameB="opls_140"}
39: type[109]={name="opls_274",nameB="opls_274"}
39: type[110]={name="opls_140",nameB="opls_140"}
39: type[111]={name="opls_140",nameB="opls_140"}
39: type[112]={name="opls_271",nameB="opls_271"}
39: type[113]={name="opls_272",nameB="opls_272"}
39: type[114]={name="opls_272",nameB="opls_272"}
39: type[115]={name="opls_235",nameB="opls_235"}
39: type[116]={name="opls_236",nameB="opls_236"}
39: type[117]={name="opls_238",nameB="opls_238"}
39: type[118]={name="opls_241",nameB="opls_241"}
39: type[119]={name="opls_224B",nameB="opls_224B"}
39: type[120]={name="opls_140",nameB="opls_140"}
39: type[121]={name="opls_136",nameB="opls_136"}
39: type[122]={name="opls_140",nameB="opls_140"}
39: type[123]={name="opls_140",nameB="opls_140"}
39: type[124]={name="opls_137",nameB="opls_137"}
39: type[125]={name="opls_140",nameB="opls_140"}
39: type[126]={name="opls_135",nameB="opls_135"}
39: type[127]={name="opls_140",nameB="opls_140"}
39: type[128]={name="opls_140",nameB="opls_140"}
39: type[129]={name="opls_140",nameB="opls_140"}
39: type[130]={name="opls_135",nameB="opls_135"}
39: type[131]={name="opls_140",nameB="opls_140"}
39: type[132]={name="opls_140",nameB="opls_140"}
39: type[133]={name="opls_140",nameB="opls_140"}
39: type[134]={name="opls_235",nameB="opls_235"}
39: type[135]={name="opls_236",nameB="opls_236"}
39: type[136]={name="opls_238",nameB="opls_238"}
39: type[137]={name="opls_241",nameB="opls_241"}
39: type[138]={name="opls_224B",nameB="opls_224B"}
39: type[139]={name="opls_140",nameB="opls_140"}
39: type[140]={name="opls_135",nameB="opls_135"}
39: type[141]={name="opls_140",nameB="opls_140"}
39: type[142]={name="opls_140",nameB="opls_140"}
39: type[143]={name="opls_140",nameB="opls_140"}
39: type[144]={name="opls_235",nameB="opls_235"}
39: type[145]={name="opls_236",nameB="opls_236"}
39: type[146]={name="opls_238",nameB="opls_238"}
39: type[147]={name="opls_241",nameB="opls_241"}
39: type[148]={name="opls_224B",nameB="opls_224B"}
39: type[149]={name="opls_140",nameB="opls_140"}
39: type[150]={name="opls_135",nameB="opls_135"}
39: type[151]={name="opls_140",nameB="opls_140"}
39: type[152]={name="opls_140",nameB="opls_140"}
39: type[153]={name="opls_140",nameB="opls_140"}
39: type[154]={name="opls_235",nameB="opls_235"}
39: type[155]={name="opls_236",nameB="opls_236"}
39: residue (10):
39: residue[0]={name="LYS", nr=1, ic=' '}
39: residue[1]={name="VAL", nr=2, ic=' '}
39: residue[2]={name="PHE", nr=3, ic=' '}
39: residue[3]={name="GLY", nr=4, ic=' '}
39: residue[4]={name="ARG", nr=5, ic=' '}
39: residue[5]={name="CYS", nr=6, ic=' '}
39: residue[6]={name="GLU", nr=7, ic=' '}
39: residue[7]={name="LEU", nr=8, ic=' '}
39: residue[8]={name="ALA", nr=9, ic=' '}
39: residue[9]={name="ALA", nr=10, ic=' '}
39: excls:
39: nr=156
39: nra=1828
39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
39: 23, 24, 25, 26}
39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
39: 14, 15, 22, 23, 24}
39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
39: 16, 17, 18, 22}
39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
39: 17, 18, 19, 20, 21}
39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
39: 19, 20, 21}
39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
39: 25, 26, 27, 28, 38}
39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
39: 30, 34, 38, 39, 40}
39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40}
39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
39: 34, 35, 36, 37, 38, 39, 40}
39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40, 41, 42, 43, 44, 58}
39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
39: 45, 46, 47, 58, 59, 60}
39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
39: 48, 50, 58, 59, 60, 61, 62}
39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60}
39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
39: 50, 51, 52, 54, 58, 59, 60}
39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
39: 52, 53, 54, 55, 56, 58}
39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
39: 54, 56, 57}
39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
39: 55, 56, 57}
39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60, 61, 62, 63, 64, 65}
39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
39: 65, 66, 67}
39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
39: 68, 69}
39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
39: 70, 71, 89}
39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
39: 72, 73, 74, 89, 90, 91}
39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
39: 75, 76, 77, 89, 90, 91, 92, 93}
39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
39: 91}
39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
39: 77, 78, 79, 80, 89, 90, 91}
39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
39: 79, 80, 81, 82, 89}
39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
39: 81, 82, 83, 86}
39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
39: 84, 85, 86, 87, 88}
39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
39: 86, 87, 88}
39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
39: 90, 91, 92, 93, 94, 95, 100}
39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
39: 95, 96, 97, 98, 100, 101, 102}
39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
39: 98, 99, 100, 101, 102, 103, 104}
39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102}
39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
39: 100, 101, 102}
39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102, 103, 104, 105, 106, 115}
39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
39: 105, 106, 107, 108, 109, 115, 116, 117}
39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
39: 115}
39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117}
39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 110, 111, 112, 113, 114, 115, 116, 117}
39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 113, 114, 115}
39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117, 118, 119, 120, 121, 134}
39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119}
39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119, 120, 121, 122, 123, 124, 134, 135, 136}
39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
39: 134}
39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136}
39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
39: 136}
39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 127, 128, 129, 130, 131, 132, 133, 134}
39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136, 137, 138, 139, 140, 144}
39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138}
39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138, 139, 140, 141, 142, 143, 144, 145, 146}
39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
39: 144}
39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
39: 141, 142, 143, 144, 145, 146, 147, 148}
39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146, 147, 148, 149, 150, 154}
39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148}
39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148, 149, 150, 151, 152, 153, 154, 155}
39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
39: 154}
39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
39: 151, 152, 153, 154, 155}
39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
39: Bond:
39: nr: 468
39: iatoms:
39: 0 type=100 (BONDS) 0 1
39: 1 type=100 (BONDS) 0 2
39: 2 type=100 (BONDS) 0 3
39: 3 type=101 (BONDS) 0 4
39: 4 type=102 (BONDS) 4 5
39: 5 type=103 (BONDS) 4 6
39: 6 type=104 (BONDS) 4 22
39: 7 type=102 (BONDS) 6 7
39: 8 type=102 (BONDS) 6 8
39: 9 type=103 (BONDS) 6 9
39: 10 type=102 (BONDS) 9 10
39: 11 type=102 (BONDS) 9 11
39: 12 type=103 (BONDS) 9 12
39: 13 type=102 (BONDS) 12 13
39: 14 type=102 (BONDS) 12 14
39: 15 type=103 (BONDS) 12 15
39: 16 type=102 (BONDS) 15 16
39: 17 type=102 (BONDS) 15 17
39: 18 type=101 (BONDS) 15 18
39: 19 type=100 (BONDS) 18 19
39: 20 type=100 (BONDS) 18 20
39: 21 type=100 (BONDS) 18 21
39: 22 type=105 (BONDS) 22 23
39: 23 type=106 (BONDS) 22 24
39: 24 type=100 (BONDS) 24 25
39: 25 type=107 (BONDS) 24 26
39: 26 type=102 (BONDS) 26 27
39: 27 type=103 (BONDS) 26 28
39: 28 type=104 (BONDS) 26 38
39: 29 type=102 (BONDS) 28 29
39: 30 type=103 (BONDS) 28 30
39: 31 type=103 (BONDS) 28 34
39: 32 type=102 (BONDS) 30 31
39: 33 type=102 (BONDS) 30 32
39: 34 type=102 (BONDS) 30 33
39: 35 type=102 (BONDS) 34 35
39: 36 type=102 (BONDS) 34 36
39: 37 type=102 (BONDS) 34 37
39: 38 type=105 (BONDS) 38 39
39: 39 type=106 (BONDS) 38 40
39: 40 type=100 (BONDS) 40 41
39: 41 type=107 (BONDS) 40 42
39: 42 type=102 (BONDS) 42 43
39: 43 type=103 (BONDS) 42 44
39: 44 type=104 (BONDS) 42 58
39: 45 type=102 (BONDS) 44 45
39: 46 type=102 (BONDS) 44 46
39: 47 type=108 (BONDS) 44 47
39: 48 type=109 (BONDS) 47 48
39: 49 type=109 (BONDS) 47 50
39: 50 type=110 (BONDS) 48 49
39: 51 type=109 (BONDS) 48 52
39: 52 type=110 (BONDS) 50 51
39: 53 type=109 (BONDS) 50 54
39: 54 type=110 (BONDS) 52 53
39: 55 type=109 (BONDS) 52 56
39: 56 type=110 (BONDS) 54 55
39: 57 type=109 (BONDS) 54 56
39: 58 type=110 (BONDS) 56 57
39: 59 type=105 (BONDS) 58 59
39: 60 type=106 (BONDS) 58 60
39: 61 type=100 (BONDS) 60 61
39: 62 type=107 (BONDS) 60 62
39: 63 type=102 (BONDS) 62 63
39: 64 type=102 (BONDS) 62 64
39: 65 type=104 (BONDS) 62 65
39: 66 type=105 (BONDS) 65 66
39: 67 type=106 (BONDS) 65 67
39: 68 type=100 (BONDS) 67 68
39: 69 type=107 (BONDS) 67 69
39: 70 type=102 (BONDS) 69 70
39: 71 type=103 (BONDS) 69 71
39: 72 type=104 (BONDS) 69 89
39: 73 type=102 (BONDS) 71 72
39: 74 type=102 (BONDS) 71 73
39: 75 type=103 (BONDS) 71 74
39: 76 type=102 (BONDS) 74 75
39: 77 type=102 (BONDS) 74 76
39: 78 type=103 (BONDS) 74 77
39: 79 type=102 (BONDS) 77 78
39: 80 type=102 (BONDS) 77 79
39: 81 type=111 (BONDS) 77 80
39: 82 type=100 (BONDS) 80 81
39: 83 type=112 (BONDS) 80 82
39: 84 type=112 (BONDS) 82 83
39: 85 type=112 (BONDS) 82 86
39: 86 type=100 (BONDS) 83 84
39: 87 type=100 (BONDS) 83 85
39: 88 type=100 (BONDS) 86 87
39: 89 type=100 (BONDS) 86 88
39: 90 type=105 (BONDS) 89 90
39: 91 type=106 (BONDS) 89 91
39: 92 type=100 (BONDS) 91 92
39: 93 type=107 (BONDS) 91 93
39: 94 type=102 (BONDS) 93 94
39: 95 type=103 (BONDS) 93 95
39: 96 type=104 (BONDS) 93 100
39: 97 type=102 (BONDS) 95 96
39: 98 type=102 (BONDS) 95 97
39: 99 type=113 (BONDS) 95 98
39: 100 type=114 (BONDS) 98 99
39: 101 type=105 (BONDS) 100 101
39: 102 type=106 (BONDS) 100 102
39: 103 type=100 (BONDS) 102 103
39: 104 type=107 (BONDS) 102 104
39: 105 type=102 (BONDS) 104 105
39: 106 type=103 (BONDS) 104 106
39: 107 type=104 (BONDS) 104 115
39: 108 type=102 (BONDS) 106 107
39: 109 type=102 (BONDS) 106 108
39: 110 type=103 (BONDS) 106 109
39: 111 type=102 (BONDS) 109 110
39: 112 type=102 (BONDS) 109 111
39: 113 type=104 (BONDS) 109 112
39: 114 type=115 (BONDS) 112 113
39: 115 type=115 (BONDS) 112 114
39: 116 type=105 (BONDS) 115 116
39: 117 type=106 (BONDS) 115 117
39: 118 type=100 (BONDS) 117 118
39: 119 type=107 (BONDS) 117 119
39: 120 type=102 (BONDS) 119 120
39: 121 type=103 (BONDS) 119 121
39: 122 type=104 (BONDS) 119 134
39: 123 type=102 (BONDS) 121 122
39: 124 type=102 (BONDS) 121 123
39: 125 type=103 (BONDS) 121 124
39: 126 type=102 (BONDS) 124 125
39: 127 type=103 (BONDS) 124 126
39: 128 type=103 (BONDS) 124 130
39: 129 type=102 (BONDS) 126 127
39: 130 type=102 (BONDS) 126 128
39: 131 type=102 (BONDS) 126 129
39: 132 type=102 (BONDS) 130 131
39: 133 type=102 (BONDS) 130 132
39: 134 type=102 (BONDS) 130 133
39: 135 type=105 (BONDS) 134 135
39: 136 type=106 (BONDS) 134 136
39: 137 type=100 (BONDS) 136 137
39: 138 type=107 (BONDS) 136 138
39: 139 type=102 (BONDS) 138 139
39: 140 type=103 (BONDS) 138 140
39: 141 type=104 (BONDS) 138 144
39: 142 type=102 (BONDS) 140 141
39: 143 type=102 (BONDS) 140 142
39: 144 type=102 (BONDS) 140 143
39: 145 type=105 (BONDS) 144 145
39: 146 type=106 (BONDS) 144 146
39: 147 type=100 (BONDS) 146 147
39: 148 type=107 (BONDS) 146 148
39: 149 type=102 (BONDS) 148 149
39: 150 type=103 (BONDS) 148 150
39: 151 type=104 (BONDS) 148 154
39: 152 type=102 (BONDS) 150 151
39: 153 type=102 (BONDS) 150 152
39: 154 type=102 (BONDS) 150 153
39: 155 type=105 (BONDS) 154 155
39: G96Bond:
39: nr: 0
39: Morse:
39: nr: 0
39: Cubic Bonds:
39: nr: 0
39: Connect Bonds:
39: nr: 0
39: Harmonic Pot.:
39: nr: 0
39: FENE Bonds:
39: nr: 0
39: Tab. Bonds:
39: nr: 0
39: Tab. Bonds NC:
39: nr: 0
39: Restraint Pot.:
39: nr: 0
39: Angle:
39: nr: 1124
39: iatoms:
39: 0 type=116 (ANGLES) 1 0 2
39: 1 type=116 (ANGLES) 1 0 3
39: 2 type=116 (ANGLES) 1 0 4
39: 3 type=116 (ANGLES) 2 0 3
39: 4 type=116 (ANGLES) 2 0 4
39: 5 type=116 (ANGLES) 3 0 4
39: 6 type=116 (ANGLES) 0 4 5
39: 7 type=117 (ANGLES) 0 4 6
39: 8 type=117 (ANGLES) 0 4 22
39: 9 type=118 (ANGLES) 5 4 6
39: 10 type=116 (ANGLES) 5 4 22
39: 11 type=119 (ANGLES) 6 4 22
39: 12 type=118 (ANGLES) 4 6 7
39: 13 type=118 (ANGLES) 4 6 8
39: 14 type=120 (ANGLES) 4 6 9
39: 15 type=121 (ANGLES) 7 6 8
39: 16 type=118 (ANGLES) 7 6 9
39: 17 type=118 (ANGLES) 8 6 9
39: 18 type=118 (ANGLES) 6 9 10
39: 19 type=118 (ANGLES) 6 9 11
39: 20 type=120 (ANGLES) 6 9 12
39: 21 type=121 (ANGLES) 10 9 11
39: 22 type=118 (ANGLES) 10 9 12
39: 23 type=118 (ANGLES) 11 9 12
39: 24 type=118 (ANGLES) 9 12 13
39: 25 type=118 (ANGLES) 9 12 14
39: 26 type=120 (ANGLES) 9 12 15
39: 27 type=121 (ANGLES) 13 12 14
39: 28 type=118 (ANGLES) 13 12 15
39: 29 type=118 (ANGLES) 14 12 15
39: 30 type=118 (ANGLES) 12 15 16
39: 31 type=118 (ANGLES) 12 15 17
39: 32 type=117 (ANGLES) 12 15 18
39: 33 type=121 (ANGLES) 16 15 17
39: 34 type=116 (ANGLES) 16 15 18
39: 35 type=116 (ANGLES) 17 15 18
39: 36 type=116 (ANGLES) 15 18 19
39: 37 type=116 (ANGLES) 15 18 20
39: 38 type=116 (ANGLES) 15 18 21
39: 39 type=116 (ANGLES) 19 18 20
39: 40 type=116 (ANGLES) 19 18 21
39: 41 type=116 (ANGLES) 20 18 21
39: 42 type=122 (ANGLES) 4 22 23
39: 43 type=123 (ANGLES) 4 22 24
39: 44 type=124 (ANGLES) 23 22 24
39: 45 type=125 (ANGLES) 22 24 25
39: 46 type=126 (ANGLES) 22 24 26
39: 47 type=127 (ANGLES) 25 24 26
39: 48 type=116 (ANGLES) 24 26 27
39: 49 type=128 (ANGLES) 24 26 28
39: 50 type=129 (ANGLES) 24 26 38
39: 51 type=118 (ANGLES) 27 26 28
39: 52 type=116 (ANGLES) 27 26 38
39: 53 type=119 (ANGLES) 28 26 38
39: 54 type=118 (ANGLES) 26 28 29
39: 55 type=120 (ANGLES) 26 28 30
39: 56 type=120 (ANGLES) 26 28 34
39: 57 type=118 (ANGLES) 29 28 30
39: 58 type=118 (ANGLES) 29 28 34
39: 59 type=120 (ANGLES) 30 28 34
39: 60 type=118 (ANGLES) 28 30 31
39: 61 type=118 (ANGLES) 28 30 32
39: 62 type=118 (ANGLES) 28 30 33
39: 63 type=121 (ANGLES) 31 30 32
39: 64 type=121 (ANGLES) 31 30 33
39: 65 type=121 (ANGLES) 32 30 33
39: 66 type=118 (ANGLES) 28 34 35
39: 67 type=118 (ANGLES) 28 34 36
39: 68 type=118 (ANGLES) 28 34 37
39: 69 type=121 (ANGLES) 35 34 36
39: 70 type=121 (ANGLES) 35 34 37
39: 71 type=121 (ANGLES) 36 34 37
39: 72 type=122 (ANGLES) 26 38 39
39: 73 type=123 (ANGLES) 26 38 40
39: 74 type=124 (ANGLES) 39 38 40
39: 75 type=125 (ANGLES) 38 40 41
39: 76 type=126 (ANGLES) 38 40 42
39: 77 type=127 (ANGLES) 41 40 42
39: 78 type=116 (ANGLES) 40 42 43
39: 79 type=128 (ANGLES) 40 42 44
39: 80 type=129 (ANGLES) 40 42 58
39: 81 type=118 (ANGLES) 43 42 44
39: 82 type=116 (ANGLES) 43 42 58
39: 83 type=119 (ANGLES) 44 42 58
39: 84 type=118 (ANGLES) 42 44 45
39: 85 type=118 (ANGLES) 42 44 46
39: 86 type=130 (ANGLES) 42 44 47
39: 87 type=121 (ANGLES) 45 44 46
39: 88 type=116 (ANGLES) 45 44 47
39: 89 type=116 (ANGLES) 46 44 47
39: 90 type=131 (ANGLES) 44 47 48
39: 91 type=131 (ANGLES) 44 47 50
39: 92 type=132 (ANGLES) 48 47 50
39: 93 type=133 (ANGLES) 47 48 49
39: 94 type=132 (ANGLES) 47 48 52
39: 95 type=133 (ANGLES) 49 48 52
39: 96 type=133 (ANGLES) 47 50 51
39: 97 type=132 (ANGLES) 47 50 54
39: 98 type=133 (ANGLES) 51 50 54
39: 99 type=133 (ANGLES) 48 52 53
39: 100 type=132 (ANGLES) 48 52 56
39: 101 type=133 (ANGLES) 53 52 56
39: 102 type=133 (ANGLES) 50 54 55
39: 103 type=132 (ANGLES) 50 54 56
39: 104 type=133 (ANGLES) 55 54 56
39: 105 type=132 (ANGLES) 52 56 54
39: 106 type=133 (ANGLES) 52 56 57
39: 107 type=133 (ANGLES) 54 56 57
39: 108 type=122 (ANGLES) 42 58 59
39: 109 type=123 (ANGLES) 42 58 60
39: 110 type=124 (ANGLES) 59 58 60
39: 111 type=125 (ANGLES) 58 60 61
39: 112 type=126 (ANGLES) 58 60 62
39: 113 type=127 (ANGLES) 61 60 62
39: 114 type=116 (ANGLES) 60 62 63
39: 115 type=116 (ANGLES) 60 62 64
39: 116 type=129 (ANGLES) 60 62 65
39: 117 type=121 (ANGLES) 63 62 64
39: 118 type=116 (ANGLES) 63 62 65
39: 119 type=116 (ANGLES) 64 62 65
39: 120 type=122 (ANGLES) 62 65 66
39: 121 type=123 (ANGLES) 62 65 67
39: 122 type=124 (ANGLES) 66 65 67
39: 123 type=125 (ANGLES) 65 67 68
39: 124 type=126 (ANGLES) 65 67 69
39: 125 type=127 (ANGLES) 68 67 69
39: 126 type=116 (ANGLES) 67 69 70
39: 127 type=128 (ANGLES) 67 69 71
39: 128 type=129 (ANGLES) 67 69 89
39: 129 type=118 (ANGLES) 70 69 71
39: 130 type=116 (ANGLES) 70 69 89
39: 131 type=119 (ANGLES) 71 69 89
39: 132 type=118 (ANGLES) 69 71 72
39: 133 type=118 (ANGLES) 69 71 73
39: 134 type=120 (ANGLES) 69 71 74
39: 135 type=121 (ANGLES) 72 71 73
39: 136 type=118 (ANGLES) 72 71 74
39: 137 type=118 (ANGLES) 73 71 74
39: 138 type=118 (ANGLES) 71 74 75
39: 139 type=118 (ANGLES) 71 74 76
39: 140 type=120 (ANGLES) 71 74 77
39: 141 type=121 (ANGLES) 75 74 76
39: 142 type=118 (ANGLES) 75 74 77
39: 143 type=118 (ANGLES) 76 74 77
39: 144 type=118 (ANGLES) 74 77 78
39: 145 type=118 (ANGLES) 74 77 79
39: 146 type=117 (ANGLES) 74 77 80
39: 147 type=121 (ANGLES) 78 77 79
39: 148 type=116 (ANGLES) 78 77 80
39: 149 type=116 (ANGLES) 79 77 80
39: 150 type=134 (ANGLES) 77 80 81
39: 151 type=135 (ANGLES) 77 80 82
39: 152 type=133 (ANGLES) 81 80 82
39: 153 type=131 (ANGLES) 80 82 83
39: 154 type=131 (ANGLES) 80 82 86
39: 155 type=131 (ANGLES) 83 82 86
39: 156 type=133 (ANGLES) 82 83 84
39: 157 type=133 (ANGLES) 82 83 85
39: 158 type=133 (ANGLES) 84 83 85
39: 159 type=133 (ANGLES) 82 86 87
39: 160 type=133 (ANGLES) 82 86 88
39: 161 type=133 (ANGLES) 87 86 88
39: 162 type=122 (ANGLES) 69 89 90
39: 163 type=123 (ANGLES) 69 89 91
39: 164 type=124 (ANGLES) 90 89 91
39: 165 type=125 (ANGLES) 89 91 92
39: 166 type=126 (ANGLES) 89 91 93
39: 167 type=127 (ANGLES) 92 91 93
39: 168 type=116 (ANGLES) 91 93 94
39: 169 type=128 (ANGLES) 91 93 95
39: 170 type=129 (ANGLES) 91 93 100
39: 171 type=118 (ANGLES) 94 93 95
39: 172 type=116 (ANGLES) 94 93 100
39: 173 type=119 (ANGLES) 95 93 100
39: 174 type=118 (ANGLES) 93 95 96
39: 175 type=118 (ANGLES) 93 95 97
39: 176 type=136 (ANGLES) 93 95 98
39: 177 type=121 (ANGLES) 96 95 97
39: 178 type=116 (ANGLES) 96 95 98
39: 179 type=116 (ANGLES) 97 95 98
39: 180 type=137 (ANGLES) 95 98 99
39: 181 type=122 (ANGLES) 93 100 101
39: 182 type=123 (ANGLES) 93 100 102
39: 183 type=124 (ANGLES) 101 100 102
39: 184 type=125 (ANGLES) 100 102 103
39: 185 type=126 (ANGLES) 100 102 104
39: 186 type=127 (ANGLES) 103 102 104
39: 187 type=116 (ANGLES) 102 104 105
39: 188 type=128 (ANGLES) 102 104 106
39: 189 type=129 (ANGLES) 102 104 115
39: 190 type=118 (ANGLES) 105 104 106
39: 191 type=116 (ANGLES) 105 104 115
39: 192 type=119 (ANGLES) 106 104 115
39: 193 type=118 (ANGLES) 104 106 107
39: 194 type=118 (ANGLES) 104 106 108
39: 195 type=120 (ANGLES) 104 106 109
39: 196 type=121 (ANGLES) 107 106 108
39: 197 type=118 (ANGLES) 107 106 109
39: 198 type=118 (ANGLES) 108 106 109
39: 199 type=118 (ANGLES) 106 109 110
39: 200 type=118 (ANGLES) 106 109 111
39: 201 type=119 (ANGLES) 106 109 112
39: 202 type=121 (ANGLES) 110 109 111
39: 203 type=116 (ANGLES) 110 109 112
39: 204 type=116 (ANGLES) 111 109 112
39: 205 type=138 (ANGLES) 109 112 113
39: 206 type=138 (ANGLES) 109 112 114
39: 207 type=139 (ANGLES) 113 112 114
39: 208 type=122 (ANGLES) 104 115 116
39: 209 type=123 (ANGLES) 104 115 117
39: 210 type=124 (ANGLES) 116 115 117
39: 211 type=125 (ANGLES) 115 117 118
39: 212 type=126 (ANGLES) 115 117 119
39: 213 type=127 (ANGLES) 118 117 119
39: 214 type=116 (ANGLES) 117 119 120
39: 215 type=128 (ANGLES) 117 119 121
39: 216 type=129 (ANGLES) 117 119 134
39: 217 type=118 (ANGLES) 120 119 121
39: 218 type=116 (ANGLES) 120 119 134
39: 219 type=119 (ANGLES) 121 119 134
39: 220 type=118 (ANGLES) 119 121 122
39: 221 type=118 (ANGLES) 119 121 123
39: 222 type=120 (ANGLES) 119 121 124
39: 223 type=121 (ANGLES) 122 121 123
39: 224 type=118 (ANGLES) 122 121 124
39: 225 type=118 (ANGLES) 123 121 124
39: 226 type=118 (ANGLES) 121 124 125
39: 227 type=120 (ANGLES) 121 124 126
39: 228 type=120 (ANGLES) 121 124 130
39: 229 type=118 (ANGLES) 125 124 126
39: 230 type=118 (ANGLES) 125 124 130
39: 231 type=120 (ANGLES) 126 124 130
39: 232 type=118 (ANGLES) 124 126 127
39: 233 type=118 (ANGLES) 124 126 128
39: 234 type=118 (ANGLES) 124 126 129
39: 235 type=121 (ANGLES) 127 126 128
39: 236 type=121 (ANGLES) 127 126 129
39: 237 type=121 (ANGLES) 128 126 129
39: 238 type=118 (ANGLES) 124 130 131
39: 239 type=118 (ANGLES) 124 130 132
39: 240 type=118 (ANGLES) 124 130 133
39: 241 type=121 (ANGLES) 131 130 132
39: 242 type=121 (ANGLES) 131 130 133
39: 243 type=121 (ANGLES) 132 130 133
39: 244 type=122 (ANGLES) 119 134 135
39: 245 type=123 (ANGLES) 119 134 136
39: 246 type=124 (ANGLES) 135 134 136
39: 247 type=125 (ANGLES) 134 136 137
39: 248 type=126 (ANGLES) 134 136 138
39: 249 type=127 (ANGLES) 137 136 138
39: 250 type=116 (ANGLES) 136 138 139
39: 251 type=128 (ANGLES) 136 138 140
39: 252 type=129 (ANGLES) 136 138 144
39: 253 type=118 (ANGLES) 139 138 140
39: 254 type=116 (ANGLES) 139 138 144
39: 255 type=119 (ANGLES) 140 138 144
39: 256 type=118 (ANGLES) 138 140 141
39: 257 type=118 (ANGLES) 138 140 142
39: 258 type=118 (ANGLES) 138 140 143
39: 259 type=121 (ANGLES) 141 140 142
39: 260 type=121 (ANGLES) 141 140 143
39: 261 type=121 (ANGLES) 142 140 143
39: 262 type=122 (ANGLES) 138 144 145
39: 263 type=123 (ANGLES) 138 144 146
39: 264 type=124 (ANGLES) 145 144 146
39: 265 type=125 (ANGLES) 144 146 147
39: 266 type=126 (ANGLES) 144 146 148
39: 267 type=127 (ANGLES) 147 146 148
39: 268 type=116 (ANGLES) 146 148 149
39: 269 type=128 (ANGLES) 146 148 150
39: 270 type=129 (ANGLES) 146 148 154
39: 271 type=118 (ANGLES) 149 148 150
39: 272 type=116 (ANGLES) 149 148 154
39: 273 type=119 (ANGLES) 150 148 154
39: 274 type=118 (ANGLES) 148 150 151
39: 275 type=118 (ANGLES) 148 150 152
39: 276 type=118 (ANGLES) 148 150 153
39: 277 type=121 (ANGLES) 151 150 152
39: 278 type=121 (ANGLES) 151 150 153
39: 279 type=121 (ANGLES) 152 150 153
39: 280 type=122 (ANGLES) 148 154 155
39: G96Angle:
39: nr: 0
39: Restricted Angles:
39: nr: 0
39: Lin. Angle:
39: nr: 0
39: Bond-Cross:
39: nr: 0
39: BA-Cross:
39: nr: 0
39: U-B:
39: nr: 0
39: Quartic Angles:
39: nr: 0
39: Tab. Angles:
39: nr: 0
39: Proper Dih.:
39: nr: 145
39: iatoms:
39: 0 type=140 (PDIHS) 4 24 22 23
39: 1 type=141 (PDIHS) 22 26 24 25
39: 2 type=140 (PDIHS) 26 40 38 39
39: 3 type=141 (PDIHS) 38 42 40 41
39: 4 type=140 (PDIHS) 42 60 58 59
39: 5 type=142 (PDIHS) 44 47 50 48
39: 6 type=142 (PDIHS) 47 52 48 49
39: 7 type=142 (PDIHS) 47 54 50 51
39: 8 type=142 (PDIHS) 48 56 52 53
39: 9 type=142 (PDIHS) 50 56 54 55
39: 10 type=142 (PDIHS) 52 54 56 57
39: 11 type=141 (PDIHS) 58 62 60 61
39: 12 type=140 (PDIHS) 62 67 65 66
39: 13 type=141 (PDIHS) 65 69 67 68
39: 14 type=140 (PDIHS) 69 91 89 90
39: 15 type=141 (PDIHS) 77 82 80 81
39: 16 type=140 (PDIHS) 80 83 82 86
39: 17 type=141 (PDIHS) 82 84 83 85
39: 18 type=141 (PDIHS) 82 87 86 88
39: 19 type=141 (PDIHS) 89 93 91 92
39: 20 type=140 (PDIHS) 93 102 100 101
39: 21 type=141 (PDIHS) 100 104 102 103
39: 22 type=140 (PDIHS) 104 117 115 116
39: 23 type=140 (PDIHS) 109 113 112 114
39: 24 type=141 (PDIHS) 115 119 117 118
39: 25 type=140 (PDIHS) 119 136 134 135
39: 26 type=141 (PDIHS) 134 138 136 137
39: 27 type=140 (PDIHS) 138 146 144 145
39: 28 type=141 (PDIHS) 144 148 146 147
39: Ryckaert-Bell.:
39: nr: 1565
39: iatoms:
39: 0 type=143 (RBDIHS) 1 0 4 5
39: 1 type=144 (RBDIHS) 1 0 4 6
39: 2 type=144 (RBDIHS) 1 0 4 22
39: 3 type=143 (RBDIHS) 2 0 4 5
39: 4 type=144 (RBDIHS) 2 0 4 6
39: 5 type=144 (RBDIHS) 2 0 4 22
39: 6 type=143 (RBDIHS) 3 0 4 5
39: 7 type=144 (RBDIHS) 3 0 4 6
39: 8 type=144 (RBDIHS) 3 0 4 22
39: 9 type=145 (RBDIHS) 0 4 6 9
39: 10 type=146 (RBDIHS) 22 4 6 9
39: 11 type=147 (RBDIHS) 0 4 6 7
39: 12 type=147 (RBDIHS) 0 4 6 8
39: 13 type=148 (RBDIHS) 5 4 6 7
39: 14 type=148 (RBDIHS) 5 4 6 8
39: 15 type=148 (RBDIHS) 5 4 6 9
39: 16 type=149 (RBDIHS) 22 4 6 7
39: 17 type=149 (RBDIHS) 22 4 6 8
39: 18 type=150 (RBDIHS) 0 4 22 24
39: 19 type=151 (RBDIHS) 6 4 22 24
39: 20 type=148 (RBDIHS) 4 6 9 10
39: 21 type=148 (RBDIHS) 4 6 9 11
39: 22 type=152 (RBDIHS) 4 6 9 12
39: 23 type=148 (RBDIHS) 7 6 9 10
39: 24 type=148 (RBDIHS) 7 6 9 11
39: 25 type=148 (RBDIHS) 7 6 9 12
39: 26 type=148 (RBDIHS) 8 6 9 10
39: 27 type=148 (RBDIHS) 8 6 9 11
39: 28 type=148 (RBDIHS) 8 6 9 12
39: 29 type=148 (RBDIHS) 6 9 12 13
39: 30 type=148 (RBDIHS) 6 9 12 14
39: 31 type=152 (RBDIHS) 6 9 12 15
39: 32 type=148 (RBDIHS) 10 9 12 13
39: 33 type=148 (RBDIHS) 10 9 12 14
39: 34 type=148 (RBDIHS) 10 9 12 15
39: 35 type=148 (RBDIHS) 11 9 12 13
39: 36 type=148 (RBDIHS) 11 9 12 14
39: 37 type=148 (RBDIHS) 11 9 12 15
39: 38 type=148 (RBDIHS) 9 12 15 16
39: 39 type=148 (RBDIHS) 9 12 15 17
39: 40 type=153 (RBDIHS) 9 12 15 18
39: 41 type=148 (RBDIHS) 13 12 15 16
39: 42 type=148 (RBDIHS) 13 12 15 17
39: 43 type=154 (RBDIHS) 13 12 15 18
39: 44 type=148 (RBDIHS) 14 12 15 16
39: 45 type=148 (RBDIHS) 14 12 15 17
39: 46 type=154 (RBDIHS) 14 12 15 18
39: 47 type=144 (RBDIHS) 12 15 18 19
39: 48 type=144 (RBDIHS) 12 15 18 20
39: 49 type=144 (RBDIHS) 12 15 18 21
39: 50 type=143 (RBDIHS) 16 15 18 19
39: 51 type=143 (RBDIHS) 16 15 18 20
39: 52 type=143 (RBDIHS) 16 15 18 21
39: 53 type=143 (RBDIHS) 17 15 18 19
39: 54 type=143 (RBDIHS) 17 15 18 20
39: 55 type=143 (RBDIHS) 17 15 18 21
39: 56 type=155 (RBDIHS) 4 22 24 25
39: 57 type=156 (RBDIHS) 4 22 24 26
39: 58 type=155 (RBDIHS) 23 22 24 25
39: 59 type=157 (RBDIHS) 23 22 24 26
39: 60 type=158 (RBDIHS) 22 24 26 28
39: 61 type=159 (RBDIHS) 22 24 26 38
39: 62 type=160 (RBDIHS) 24 26 28 30
39: 63 type=160 (RBDIHS) 24 26 28 34
39: 64 type=161 (RBDIHS) 38 26 28 30
39: 65 type=161 (RBDIHS) 38 26 28 34
39: 66 type=147 (RBDIHS) 24 26 28 29
39: 67 type=148 (RBDIHS) 27 26 28 29
39: 68 type=148 (RBDIHS) 27 26 28 30
39: 69 type=148 (RBDIHS) 27 26 28 34
39: 70 type=149 (RBDIHS) 38 26 28 29
39: 71 type=150 (RBDIHS) 24 26 38 40
39: 72 type=151 (RBDIHS) 28 26 38 40
39: 73 type=148 (RBDIHS) 26 28 30 31
39: 74 type=148 (RBDIHS) 26 28 30 32
39: 75 type=148 (RBDIHS) 26 28 30 33
39: 76 type=148 (RBDIHS) 29 28 30 31
39: 77 type=148 (RBDIHS) 29 28 30 32
39: 78 type=148 (RBDIHS) 29 28 30 33
39: 79 type=148 (RBDIHS) 34 28 30 31
39: 80 type=148 (RBDIHS) 34 28 30 32
39: 81 type=148 (RBDIHS) 34 28 30 33
39: 82 type=148 (RBDIHS) 26 28 34 35
39: 83 type=148 (RBDIHS) 26 28 34 36
39: 84 type=148 (RBDIHS) 26 28 34 37
39: 85 type=148 (RBDIHS) 29 28 34 35
39: 86 type=148 (RBDIHS) 29 28 34 36
39: 87 type=148 (RBDIHS) 29 28 34 37
39: 88 type=148 (RBDIHS) 30 28 34 35
39: 89 type=148 (RBDIHS) 30 28 34 36
39: 90 type=148 (RBDIHS) 30 28 34 37
39: 91 type=155 (RBDIHS) 26 38 40 41
39: 92 type=156 (RBDIHS) 26 38 40 42
39: 93 type=155 (RBDIHS) 39 38 40 41
39: 94 type=157 (RBDIHS) 39 38 40 42
39: 95 type=158 (RBDIHS) 38 40 42 44
39: 96 type=159 (RBDIHS) 38 40 42 58
39: 97 type=147 (RBDIHS) 40 42 44 45
39: 98 type=147 (RBDIHS) 40 42 44 46
39: 99 type=162 (RBDIHS) 40 42 44 47
39: 100 type=148 (RBDIHS) 43 42 44 45
39: 101 type=148 (RBDIHS) 43 42 44 46
39: 102 type=163 (RBDIHS) 43 42 44 47
39: 103 type=149 (RBDIHS) 58 42 44 45
39: 104 type=149 (RBDIHS) 58 42 44 46
39: 105 type=164 (RBDIHS) 58 42 44 47
39: 106 type=150 (RBDIHS) 40 42 58 60
39: 107 type=151 (RBDIHS) 44 42 58 60
39: 108 type=165 (RBDIHS) 44 47 48 49
39: 109 type=165 (RBDIHS) 44 47 48 52
39: 110 type=165 (RBDIHS) 50 47 48 49
39: 111 type=165 (RBDIHS) 50 47 48 52
39: 112 type=165 (RBDIHS) 44 47 50 51
39: 113 type=165 (RBDIHS) 44 47 50 54
39: 114 type=165 (RBDIHS) 48 47 50 51
39: 115 type=165 (RBDIHS) 48 47 50 54
39: 116 type=165 (RBDIHS) 47 48 52 53
39: 117 type=165 (RBDIHS) 47 48 52 56
39: 118 type=165 (RBDIHS) 49 48 52 53
39: 119 type=165 (RBDIHS) 49 48 52 56
39: 120 type=165 (RBDIHS) 47 50 54 55
39: 121 type=165 (RBDIHS) 47 50 54 56
39: 122 type=165 (RBDIHS) 51 50 54 55
39: 123 type=165 (RBDIHS) 51 50 54 56
39: 124 type=165 (RBDIHS) 48 52 56 54
39: 125 type=165 (RBDIHS) 48 52 56 57
39: 126 type=165 (RBDIHS) 53 52 56 54
39: 127 type=165 (RBDIHS) 53 52 56 57
39: 128 type=165 (RBDIHS) 50 54 56 52
39: 129 type=165 (RBDIHS) 50 54 56 57
39: 130 type=165 (RBDIHS) 55 54 56 52
39: 131 type=165 (RBDIHS) 55 54 56 57
39: 132 type=155 (RBDIHS) 42 58 60 61
39: 133 type=156 (RBDIHS) 42 58 60 62
39: 134 type=155 (RBDIHS) 59 58 60 61
39: 135 type=157 (RBDIHS) 59 58 60 62
39: 136 type=159 (RBDIHS) 58 60 62 65
39: 137 type=150 (RBDIHS) 60 62 65 67
39: 138 type=155 (RBDIHS) 62 65 67 68
39: 139 type=156 (RBDIHS) 62 65 67 69
39: 140 type=155 (RBDIHS) 66 65 67 68
39: 141 type=157 (RBDIHS) 66 65 67 69
39: 142 type=158 (RBDIHS) 65 67 69 71
39: 143 type=159 (RBDIHS) 65 67 69 89
39: 144 type=166 (RBDIHS) 67 69 71 74
39: 145 type=167 (RBDIHS) 89 69 71 74
39: 146 type=147 (RBDIHS) 67 69 71 72
39: 147 type=147 (RBDIHS) 67 69 71 73
39: 148 type=148 (RBDIHS) 70 69 71 72
39: 149 type=148 (RBDIHS) 70 69 71 73
39: 150 type=148 (RBDIHS) 70 69 71 74
39: 151 type=149 (RBDIHS) 89 69 71 72
39: 152 type=149 (RBDIHS) 89 69 71 73
39: 153 type=150 (RBDIHS) 67 69 89 91
39: 154 type=151 (RBDIHS) 71 69 89 91
39: 155 type=148 (RBDIHS) 69 71 74 75
39: 156 type=148 (RBDIHS) 69 71 74 76
39: 157 type=152 (RBDIHS) 69 71 74 77
39: 158 type=148 (RBDIHS) 72 71 74 75
39: 159 type=148 (RBDIHS) 72 71 74 76
39: 160 type=148 (RBDIHS) 72 71 74 77
39: 161 type=148 (RBDIHS) 73 71 74 75
39: 162 type=148 (RBDIHS) 73 71 74 76
39: 163 type=148 (RBDIHS) 73 71 74 77
39: 164 type=148 (RBDIHS) 71 74 77 78
39: 165 type=148 (RBDIHS) 71 74 77 79
39: 166 type=153 (RBDIHS) 71 74 77 80
39: 167 type=148 (RBDIHS) 75 74 77 78
39: 168 type=148 (RBDIHS) 75 74 77 79
39: 169 type=168 (RBDIHS) 75 74 77 80
39: 170 type=148 (RBDIHS) 76 74 77 78
39: 171 type=148 (RBDIHS) 76 74 77 79
39: 172 type=168 (RBDIHS) 76 74 77 80
39: 173 type=169 (RBDIHS) 74 77 80 81
39: 174 type=170 (RBDIHS) 74 77 80 82
39: 175 type=171 (RBDIHS) 78 77 80 82
39: 176 type=171 (RBDIHS) 79 77 80 82
39: 177 type=172 (RBDIHS) 77 80 82 83
39: 178 type=172 (RBDIHS) 77 80 82 86
39: 179 type=173 (RBDIHS) 81 80 82 83
39: 180 type=173 (RBDIHS) 81 80 82 86
39: 181 type=173 (RBDIHS) 80 82 83 84
39: 182 type=173 (RBDIHS) 80 82 83 85
39: 183 type=173 (RBDIHS) 86 82 83 84
39: 184 type=173 (RBDIHS) 86 82 83 85
39: 185 type=173 (RBDIHS) 80 82 86 87
39: 186 type=173 (RBDIHS) 80 82 86 88
39: 187 type=173 (RBDIHS) 83 82 86 87
39: 188 type=173 (RBDIHS) 83 82 86 88
39: 189 type=155 (RBDIHS) 69 89 91 92
39: 190 type=156 (RBDIHS) 69 89 91 93
39: 191 type=155 (RBDIHS) 90 89 91 92
39: 192 type=157 (RBDIHS) 90 89 91 93
39: 193 type=158 (RBDIHS) 89 91 93 95
39: 194 type=159 (RBDIHS) 89 91 93 100
39: 195 type=174 (RBDIHS) 91 93 95 98
39: 196 type=175 (RBDIHS) 100 93 95 98
39: 197 type=147 (RBDIHS) 91 93 95 96
39: 198 type=147 (RBDIHS) 91 93 95 97
39: 199 type=148 (RBDIHS) 94 93 95 96
39: 200 type=148 (RBDIHS) 94 93 95 97
39: 201 type=176 (RBDIHS) 94 93 95 98
39: 202 type=149 (RBDIHS) 100 93 95 96
39: 203 type=149 (RBDIHS) 100 93 95 97
39: 204 type=150 (RBDIHS) 91 93 100 102
39: 205 type=151 (RBDIHS) 95 93 100 102
39: 206 type=177 (RBDIHS) 93 95 98 99
39: 207 type=178 (RBDIHS) 96 95 98 99
39: 208 type=178 (RBDIHS) 97 95 98 99
39: 209 type=155 (RBDIHS) 93 100 102 103
39: 210 type=156 (RBDIHS) 93 100 102 104
39: 211 type=155 (RBDIHS) 101 100 102 103
39: 212 type=157 (RBDIHS) 101 100 102 104
39: 213 type=158 (RBDIHS) 100 102 104 106
39: 214 type=159 (RBDIHS) 100 102 104 115
39: 215 type=179 (RBDIHS) 102 104 106 109
39: 216 type=180 (RBDIHS) 115 104 106 109
39: 217 type=147 (RBDIHS) 102 104 106 107
39: 218 type=147 (RBDIHS) 102 104 106 108
39: 219 type=148 (RBDIHS) 105 104 106 107
39: 220 type=148 (RBDIHS) 105 104 106 108
39: 221 type=148 (RBDIHS) 105 104 106 109
39: 222 type=149 (RBDIHS) 115 104 106 107
39: 223 type=149 (RBDIHS) 115 104 106 108
39: 224 type=150 (RBDIHS) 102 104 115 117
39: 225 type=151 (RBDIHS) 106 104 115 117
39: 226 type=148 (RBDIHS) 104 106 109 110
39: 227 type=148 (RBDIHS) 104 106 109 111
39: 228 type=181 (RBDIHS) 104 106 109 112
39: 229 type=148 (RBDIHS) 107 106 109 110
39: 230 type=148 (RBDIHS) 107 106 109 111
39: 231 type=182 (RBDIHS) 107 106 109 112
39: 232 type=148 (RBDIHS) 108 106 109 110
39: 233 type=148 (RBDIHS) 108 106 109 111
39: 234 type=182 (RBDIHS) 108 106 109 112
39: 235 type=183 (RBDIHS) 106 109 112 113
39: 236 type=183 (RBDIHS) 106 109 112 114
39: 237 type=155 (RBDIHS) 104 115 117 118
39: 238 type=156 (RBDIHS) 104 115 117 119
39: 239 type=155 (RBDIHS) 116 115 117 118
39: 240 type=157 (RBDIHS) 116 115 117 119
39: 241 type=158 (RBDIHS) 115 117 119 121
39: 242 type=159 (RBDIHS) 115 117 119 134
39: 243 type=184 (RBDIHS) 117 119 121 124
39: 244 type=185 (RBDIHS) 134 119 121 124
39: 245 type=147 (RBDIHS) 117 119 121 122
39: 246 type=147 (RBDIHS) 117 119 121 123
39: 247 type=148 (RBDIHS) 120 119 121 122
39: 248 type=148 (RBDIHS) 120 119 121 123
39: 249 type=148 (RBDIHS) 120 119 121 124
39: 250 type=149 (RBDIHS) 134 119 121 122
39: 251 type=149 (RBDIHS) 134 119 121 123
39: 252 type=150 (RBDIHS) 117 119 134 136
39: 253 type=151 (RBDIHS) 121 119 134 136
39: 254 type=148 (RBDIHS) 119 121 124 125
39: 255 type=152 (RBDIHS) 119 121 124 126
39: 256 type=152 (RBDIHS) 119 121 124 130
39: 257 type=148 (RBDIHS) 122 121 124 125
39: 258 type=148 (RBDIHS) 122 121 124 126
39: 259 type=148 (RBDIHS) 122 121 124 130
39: 260 type=148 (RBDIHS) 123 121 124 125
39: 261 type=148 (RBDIHS) 123 121 124 126
39: 262 type=148 (RBDIHS) 123 121 124 130
39: 263 type=148 (RBDIHS) 121 124 126 127
39: 264 type=148 (RBDIHS) 121 124 126 128
39: 265 type=148 (RBDIHS) 121 124 126 129
39: 266 type=148 (RBDIHS) 125 124 126 127
39: 267 type=148 (RBDIHS) 125 124 126 128
39: 268 type=148 (RBDIHS) 125 124 126 129
39: 269 type=148 (RBDIHS) 130 124 126 127
39: 270 type=148 (RBDIHS) 130 124 126 128
39: 271 type=148 (RBDIHS) 130 124 126 129
39: 272 type=148 (RBDIHS) 121 124 130 131
39: 273 type=148 (RBDIHS) 121 124 130 132
39: 274 type=148 (RBDIHS) 121 124 130 133
39: 275 type=148 (RBDIHS) 125 124 130 131
39: 276 type=148 (RBDIHS) 125 124 130 132
39: 277 type=148 (RBDIHS) 125 124 130 133
39: 278 type=148 (RBDIHS) 126 124 130 131
39: 279 type=148 (RBDIHS) 126 124 130 132
39: 280 type=148 (RBDIHS) 126 124 130 133
39: 281 type=155 (RBDIHS) 119 134 136 137
39: 282 type=156 (RBDIHS) 119 134 136 138
39: 283 type=155 (RBDIHS) 135 134 136 137
39: 284 type=157 (RBDIHS) 135 134 136 138
39: 285 type=158 (RBDIHS) 134 136 138 140
39: 286 type=159 (RBDIHS) 134 136 138 144
39: 287 type=147 (RBDIHS) 136 138 140 141
39: 288 type=147 (RBDIHS) 136 138 140 142
39: 289 type=147 (RBDIHS) 136 138 140 143
39: 290 type=148 (RBDIHS) 139 138 140 141
39: 291 type=148 (RBDIHS) 139 138 140 142
39: 292 type=148 (RBDIHS) 139 138 140 143
39: 293 type=149 (RBDIHS) 144 138 140 141
39: 294 type=149 (RBDIHS) 144 138 140 142
39: 295 type=149 (RBDIHS) 144 138 140 143
39: 296 type=150 (RBDIHS) 136 138 144 146
39: 297 type=151 (RBDIHS) 140 138 144 146
39: 298 type=155 (RBDIHS) 138 144 146 147
39: 299 type=156 (RBDIHS) 138 144 146 148
39: 300 type=155 (RBDIHS) 145 144 146 147
39: 301 type=157 (RBDIHS) 145 144 146 148
39: 302 type=158 (RBDIHS) 144 146 148 150
39: 303 type=159 (RBDIHS) 144 146 148 154
39: 304 type=147 (RBDIHS) 146 148 150 151
39: 305 type=147 (RBDIHS) 146 148 150 152
39: 306 type=147 (RBDIHS) 146 148 150 153
39: 307 type=148 (RBDIHS) 149 148 150 151
39: 308 type=148 (RBDIHS) 149 148 150 152
39: 309 type=148 (RBDIHS) 149 148 150 153
39: 310 type=149 (RBDIHS) 154 148 150 151
39: 311 type=149 (RBDIHS) 154 148 150 152
39: 312 type=149 (RBDIHS) 154 148 150 153
39: Restricted Dih.:
39: nr: 0
39: CBT Dih.:
39: nr: 0
39: Fourier Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Tab. Dih.:
39: nr: 0
39: CMAP Dih.:
39: nr: 0
39: GB 1-2 Pol. (unused):
39: nr: 0
39: GB 1-3 Pol. (unused):
39: nr: 0
39: GB 1-4 Pol. (unused):
39: nr: 0
39: GB Polarization (unused):
39: nr: 0
39: Nonpolar Sol. (unused):
39: nr: 0
39: LJ-14:
39: nr: 1197
39: iatoms:
39: 0 type=186 (LJ14) 0 7
39: 1 type=186 (LJ14) 0 8
39: 2 type=187 (LJ14) 0 9
39: 3 type=188 (LJ14) 0 23
39: 4 type=189 (LJ14) 0 24
39: 5 type=190 (LJ14) 1 5
39: 6 type=190 (LJ14) 1 6
39: 7 type=190 (LJ14) 1 22
39: 8 type=190 (LJ14) 2 5
39: 9 type=190 (LJ14) 2 6
39: 10 type=190 (LJ14) 2 22
39: 11 type=190 (LJ14) 3 5
39: 12 type=190 (LJ14) 3 6
39: 13 type=190 (LJ14) 3 22
39: 14 type=191 (LJ14) 4 10
39: 15 type=191 (LJ14) 4 11
39: 16 type=192 (LJ14) 4 12
39: 17 type=190 (LJ14) 4 25
39: 18 type=192 (LJ14) 4 26
39: 19 type=193 (LJ14) 5 7
39: 20 type=193 (LJ14) 5 8
39: 21 type=191 (LJ14) 5 9
39: 22 type=194 (LJ14) 5 23
39: 23 type=186 (LJ14) 5 24
39: 24 type=191 (LJ14) 6 13
39: 25 type=191 (LJ14) 6 14
39: 26 type=192 (LJ14) 6 15
39: 27 type=195 (LJ14) 6 23
39: 28 type=187 (LJ14) 6 24
39: 29 type=193 (LJ14) 7 10
39: 30 type=193 (LJ14) 7 11
39: 31 type=191 (LJ14) 7 12
39: 32 type=196 (LJ14) 7 22
39: 33 type=193 (LJ14) 8 10
39: 34 type=193 (LJ14) 8 11
39: 35 type=191 (LJ14) 8 12
39: 36 type=196 (LJ14) 8 22
39: 37 type=191 (LJ14) 9 16
39: 38 type=191 (LJ14) 9 17
39: 39 type=187 (LJ14) 9 18
39: 40 type=197 (LJ14) 9 22
39: 41 type=193 (LJ14) 10 13
39: 42 type=193 (LJ14) 10 14
39: 43 type=191 (LJ14) 10 15
39: 44 type=193 (LJ14) 11 13
39: 45 type=193 (LJ14) 11 14
39: 46 type=191 (LJ14) 11 15
39: 47 type=190 (LJ14) 12 19
39: 48 type=190 (LJ14) 12 20
39: 49 type=190 (LJ14) 12 21
39: 50 type=193 (LJ14) 13 16
39: 51 type=193 (LJ14) 13 17
39: 52 type=186 (LJ14) 13 18
39: 53 type=193 (LJ14) 14 16
39: 54 type=193 (LJ14) 14 17
39: 55 type=186 (LJ14) 14 18
39: 56 type=190 (LJ14) 16 19
39: 57 type=190 (LJ14) 16 20
39: 58 type=190 (LJ14) 16 21
39: 59 type=190 (LJ14) 17 19
39: 60 type=190 (LJ14) 17 20
39: 61 type=190 (LJ14) 17 21
39: 62 type=196 (LJ14) 22 27
39: 63 type=197 (LJ14) 22 28
39: 64 type=198 (LJ14) 22 38
39: 65 type=190 (LJ14) 23 25
39: 66 type=195 (LJ14) 23 26
39: 67 type=186 (LJ14) 24 29
39: 68 type=187 (LJ14) 24 30
39: 69 type=187 (LJ14) 24 34
39: 70 type=188 (LJ14) 24 39
39: 71 type=189 (LJ14) 24 40
39: 72 type=190 (LJ14) 25 27
39: 73 type=190 (LJ14) 25 28
39: 74 type=190 (LJ14) 25 38
39: 75 type=191 (LJ14) 26 31
39: 76 type=191 (LJ14) 26 32
39: 77 type=191 (LJ14) 26 33
39: 78 type=191 (LJ14) 26 35
39: 79 type=191 (LJ14) 26 36
39: 80 type=191 (LJ14) 26 37
39: 81 type=190 (LJ14) 26 41
39: 82 type=192 (LJ14) 26 42
39: 83 type=193 (LJ14) 27 29
39: 84 type=191 (LJ14) 27 30
39: 85 type=191 (LJ14) 27 34
39: 86 type=194 (LJ14) 27 39
39: 87 type=186 (LJ14) 27 40
39: 88 type=195 (LJ14) 28 39
39: 89 type=187 (LJ14) 28 40
39: 90 type=193 (LJ14) 29 31
39: 91 type=193 (LJ14) 29 32
39: 92 type=193 (LJ14) 29 33
39: 93 type=193 (LJ14) 29 35
39: 94 type=193 (LJ14) 29 36
39: 95 type=193 (LJ14) 29 37
39: 96 type=196 (LJ14) 29 38
39: 97 type=191 (LJ14) 30 35
39: 98 type=191 (LJ14) 30 36
39: 99 type=191 (LJ14) 30 37
39: 100 type=197 (LJ14) 30 38
39: 101 type=191 (LJ14) 31 34
39: 102 type=191 (LJ14) 32 34
39: 103 type=191 (LJ14) 33 34
39: 104 type=197 (LJ14) 34 38
39: 105 type=196 (LJ14) 38 43
39: 106 type=197 (LJ14) 38 44
39: 107 type=198 (LJ14) 38 58
39: 108 type=190 (LJ14) 39 41
39: 109 type=195 (LJ14) 39 42
39: 110 type=186 (LJ14) 40 45
39: 111 type=186 (LJ14) 40 46
39: 112 type=199 (LJ14) 40 47
39: 113 type=188 (LJ14) 40 59
39: 114 type=189 (LJ14) 40 60
39: 115 type=190 (LJ14) 41 43
39: 116 type=190 (LJ14) 41 44
39: 117 type=190 (LJ14) 41 58
39: 118 type=200 (LJ14) 42 48
39: 119 type=200 (LJ14) 42 50
39: 120 type=190 (LJ14) 42 61
39: 121 type=192 (LJ14) 42 62
39: 122 type=193 (LJ14) 43 45
39: 123 type=193 (LJ14) 43 46
39: 124 type=201 (LJ14) 43 47
39: 125 type=194 (LJ14) 43 59
39: 126 type=186 (LJ14) 43 60
39: 127 type=202 (LJ14) 44 49
39: 128 type=202 (LJ14) 44 51
39: 129 type=200 (LJ14) 44 52
39: 130 type=200 (LJ14) 44 54
39: 131 type=195 (LJ14) 44 59
39: 132 type=187 (LJ14) 44 60
39: 133 type=201 (LJ14) 45 48
39: 134 type=201 (LJ14) 45 50
39: 135 type=196 (LJ14) 45 58
39: 136 type=201 (LJ14) 46 48
39: 137 type=201 (LJ14) 46 50
39: 138 type=196 (LJ14) 46 58
39: 139 type=203 (LJ14) 47 53
39: 140 type=203 (LJ14) 47 55
39: 141 type=204 (LJ14) 47 56
39: 142 type=205 (LJ14) 47 58
39: 143 type=203 (LJ14) 48 51
39: 144 type=204 (LJ14) 48 54
39: 145 type=203 (LJ14) 48 57
39: 146 type=203 (LJ14) 49 50
39: 147 type=206 (LJ14) 49 53
39: 148 type=203 (LJ14) 49 56
39: 149 type=204 (LJ14) 50 52
39: 150 type=203 (LJ14) 50 57
39: 151 type=206 (LJ14) 51 55
39: 152 type=203 (LJ14) 51 56
39: 153 type=203 (LJ14) 52 55
39: 154 type=203 (LJ14) 53 54
39: 155 type=206 (LJ14) 53 57
39: 156 type=206 (LJ14) 55 57
39: 157 type=196 (LJ14) 58 63
39: 158 type=196 (LJ14) 58 64
39: 159 type=198 (LJ14) 58 65
39: 160 type=190 (LJ14) 59 61
39: 161 type=195 (LJ14) 59 62
39: 162 type=188 (LJ14) 60 66
39: 163 type=189 (LJ14) 60 67
39: 164 type=190 (LJ14) 61 63
39: 165 type=190 (LJ14) 61 64
39: 166 type=190 (LJ14) 61 65
39: 167 type=190 (LJ14) 62 68
39: 168 type=192 (LJ14) 62 69
39: 169 type=194 (LJ14) 63 66
39: 170 type=186 (LJ14) 63 67
39: 171 type=194 (LJ14) 64 66
39: 172 type=186 (LJ14) 64 67
39: 173 type=196 (LJ14) 65 70
39: 174 type=197 (LJ14) 65 71
39: 175 type=198 (LJ14) 65 89
39: 176 type=190 (LJ14) 66 68
39: 177 type=195 (LJ14) 66 69
39: 178 type=186 (LJ14) 67 72
39: 179 type=186 (LJ14) 67 73
39: 180 type=187 (LJ14) 67 74
39: 181 type=188 (LJ14) 67 90
39: 182 type=189 (LJ14) 67 91
39: 183 type=190 (LJ14) 68 70
39: 184 type=190 (LJ14) 68 71
39: 185 type=190 (LJ14) 68 89
39: 186 type=191 (LJ14) 69 75
39: 187 type=191 (LJ14) 69 76
39: 188 type=192 (LJ14) 69 77
39: 189 type=190 (LJ14) 69 92
39: 190 type=192 (LJ14) 69 93
39: 191 type=193 (LJ14) 70 72
39: 192 type=193 (LJ14) 70 73
39: 193 type=191 (LJ14) 70 74
39: 194 type=194 (LJ14) 70 90
39: 195 type=186 (LJ14) 70 91
39: 196 type=191 (LJ14) 71 78
39: 197 type=191 (LJ14) 71 79
39: 198 type=187 (LJ14) 71 80
39: 199 type=195 (LJ14) 71 90
39: 200 type=187 (LJ14) 71 91
39: 201 type=193 (LJ14) 72 75
39: 202 type=193 (LJ14) 72 76
39: 203 type=191 (LJ14) 72 77
39: 204 type=196 (LJ14) 72 89
39: 205 type=193 (LJ14) 73 75
39: 206 type=193 (LJ14) 73 76
39: 207 type=191 (LJ14) 73 77
39: 208 type=196 (LJ14) 73 89
39: 209 type=190 (LJ14) 74 81
39: 210 type=207 (LJ14) 74 82
39: 211 type=197 (LJ14) 74 89
39: 212 type=193 (LJ14) 75 78
39: 213 type=193 (LJ14) 75 79
39: 214 type=186 (LJ14) 75 80
39: 215 type=193 (LJ14) 76 78
39: 216 type=193 (LJ14) 76 79
39: 217 type=186 (LJ14) 76 80
39: 218 type=187 (LJ14) 77 83
39: 219 type=187 (LJ14) 77 86
39: 220 type=190 (LJ14) 78 81
39: 221 type=208 (LJ14) 78 82
39: 222 type=190 (LJ14) 79 81
39: 223 type=208 (LJ14) 79 82
39: 224 type=190 (LJ14) 80 84
39: 225 type=190 (LJ14) 80 85
39: 226 type=190 (LJ14) 80 87
39: 227 type=190 (LJ14) 80 88
39: 228 type=190 (LJ14) 81 83
39: 229 type=190 (LJ14) 81 86
39: 230 type=190 (LJ14) 83 87
39: 231 type=190 (LJ14) 83 88
39: 232 type=190 (LJ14) 84 86
39: 233 type=190 (LJ14) 85 86
39: 234 type=196 (LJ14) 89 94
39: 235 type=197 (LJ14) 89 95
39: 236 type=198 (LJ14) 89 100
39: 237 type=190 (LJ14) 90 92
39: 238 type=195 (LJ14) 90 93
39: 239 type=186 (LJ14) 91 96
39: 240 type=186 (LJ14) 91 97
39: 241 type=209 (LJ14) 91 98
39: 242 type=188 (LJ14) 91 101
39: 243 type=189 (LJ14) 91 102
39: 244 type=190 (LJ14) 92 94
39: 245 type=190 (LJ14) 92 95
39: 246 type=190 (LJ14) 92 100
39: 247 type=190 (LJ14) 93 99
39: 248 type=190 (LJ14) 93 103
39: 249 type=192 (LJ14) 93 104
39: 250 type=193 (LJ14) 94 96
39: 251 type=193 (LJ14) 94 97
39: 252 type=210 (LJ14) 94 98
39: 253 type=194 (LJ14) 94 101
39: 254 type=186 (LJ14) 94 102
39: 255 type=195 (LJ14) 95 101
39: 256 type=187 (LJ14) 95 102
39: 257 type=190 (LJ14) 96 99
39: 258 type=196 (LJ14) 96 100
39: 259 type=190 (LJ14) 97 99
39: 260 type=196 (LJ14) 97 100
39: 261 type=211 (LJ14) 98 100
39: 262 type=196 (LJ14) 100 105
39: 263 type=197 (LJ14) 100 106
39: 264 type=198 (LJ14) 100 115
39: 265 type=190 (LJ14) 101 103
39: 266 type=195 (LJ14) 101 104
39: 267 type=186 (LJ14) 102 107
39: 268 type=186 (LJ14) 102 108
39: 269 type=187 (LJ14) 102 109
39: 270 type=188 (LJ14) 102 116
39: 271 type=189 (LJ14) 102 117
39: 272 type=190 (LJ14) 103 105
39: 273 type=190 (LJ14) 103 106
39: 274 type=190 (LJ14) 103 115
39: 275 type=191 (LJ14) 104 110
39: 276 type=191 (LJ14) 104 111
39: 277 type=197 (LJ14) 104 112
39: 278 type=190 (LJ14) 104 118
39: 279 type=192 (LJ14) 104 119
39: 280 type=193 (LJ14) 105 107
39: 281 type=193 (LJ14) 105 108
39: 282 type=191 (LJ14) 105 109
39: 283 type=194 (LJ14) 105 116
39: 284 type=186 (LJ14) 105 117
39: 285 type=195 (LJ14) 106 113
39: 286 type=195 (LJ14) 106 114
39: 287 type=195 (LJ14) 106 116
39: 288 type=187 (LJ14) 106 117
39: 289 type=193 (LJ14) 107 110
39: 290 type=193 (LJ14) 107 111
39: 291 type=196 (LJ14) 107 112
39: 292 type=196 (LJ14) 107 115
39: 293 type=193 (LJ14) 108 110
39: 294 type=193 (LJ14) 108 111
39: 295 type=196 (LJ14) 108 112
39: 296 type=196 (LJ14) 108 115
39: 297 type=197 (LJ14) 109 115
39: 298 type=194 (LJ14) 110 113
39: 299 type=194 (LJ14) 110 114
39: 300 type=194 (LJ14) 111 113
39: 301 type=194 (LJ14) 111 114
39: 302 type=196 (LJ14) 115 120
39: 303 type=197 (LJ14) 115 121
39: 304 type=198 (LJ14) 115 134
39: 305 type=190 (LJ14) 116 118
39: 306 type=195 (LJ14) 116 119
39: 307 type=186 (LJ14) 117 122
39: 308 type=186 (LJ14) 117 123
39: 309 type=187 (LJ14) 117 124
39: 310 type=188 (LJ14) 117 135
39: 311 type=189 (LJ14) 117 136
39: 312 type=190 (LJ14) 118 120
39: 313 type=190 (LJ14) 118 121
39: 314 type=190 (LJ14) 118 134
39: 315 type=191 (LJ14) 119 125
39: 316 type=192 (LJ14) 119 126
39: 317 type=192 (LJ14) 119 130
39: 318 type=190 (LJ14) 119 137
39: 319 type=192 (LJ14) 119 138
39: 320 type=193 (LJ14) 120 122
39: 321 type=193 (LJ14) 120 123
39: 322 type=191 (LJ14) 120 124
39: 323 type=194 (LJ14) 120 135
39: 324 type=186 (LJ14) 120 136
39: 325 type=191 (LJ14) 121 127
39: 326 type=191 (LJ14) 121 128
39: 327 type=191 (LJ14) 121 129
39: 328 type=191 (LJ14) 121 131
39: 329 type=191 (LJ14) 121 132
39: 330 type=191 (LJ14) 121 133
39: 331 type=195 (LJ14) 121 135
39: 332 type=187 (LJ14) 121 136
39: 333 type=193 (LJ14) 122 125
39: 334 type=191 (LJ14) 122 126
39: 335 type=191 (LJ14) 122 130
39: 336 type=196 (LJ14) 122 134
39: 337 type=193 (LJ14) 123 125
39: 338 type=191 (LJ14) 123 126
39: 339 type=191 (LJ14) 123 130
39: 340 type=196 (LJ14) 123 134
39: 341 type=197 (LJ14) 124 134
39: 342 type=193 (LJ14) 125 127
39: 343 type=193 (LJ14) 125 128
39: 344 type=193 (LJ14) 125 129
39: 345 type=193 (LJ14) 125 131
39: 346 type=193 (LJ14) 125 132
39: 347 type=193 (LJ14) 125 133
39: 348 type=191 (LJ14) 126 131
39: 349 type=191 (LJ14) 126 132
39: 350 type=191 (LJ14) 126 133
39: 351 type=191 (LJ14) 127 130
39: 352 type=191 (LJ14) 128 130
39: 353 type=191 (LJ14) 129 130
39: 354 type=196 (LJ14) 134 139
39: 355 type=197 (LJ14) 134 140
39: 356 type=198 (LJ14) 134 144
39: 357 type=190 (LJ14) 135 137
39: 358 type=195 (LJ14) 135 138
39: 359 type=186 (LJ14) 136 141
39: 360 type=186 (LJ14) 136 142
39: 361 type=186 (LJ14) 136 143
39: 362 type=188 (LJ14) 136 145
39: 363 type=189 (LJ14) 136 146
39: 364 type=190 (LJ14) 137 139
39: 365 type=190 (LJ14) 137 140
39: 366 type=190 (LJ14) 137 144
39: 367 type=190 (LJ14) 138 147
39: 368 type=192 (LJ14) 138 148
39: 369 type=193 (LJ14) 139 141
39: 370 type=193 (LJ14) 139 142
39: 371 type=193 (LJ14) 139 143
39: 372 type=194 (LJ14) 139 145
39: 373 type=186 (LJ14) 139 146
39: 374 type=195 (LJ14) 140 145
39: 375 type=187 (LJ14) 140 146
39: 376 type=196 (LJ14) 141 144
39: 377 type=196 (LJ14) 142 144
39: 378 type=196 (LJ14) 143 144
39: 379 type=196 (LJ14) 144 149
39: 380 type=197 (LJ14) 144 150
39: 381 type=198 (LJ14) 144 154
39: 382 type=190 (LJ14) 145 147
39: 383 type=195 (LJ14) 145 148
39: 384 type=186 (LJ14) 146 151
39: 385 type=186 (LJ14) 146 152
39: 386 type=186 (LJ14) 146 153
39: 387 type=188 (LJ14) 146 155
39: 388 type=190 (LJ14) 147 149
39: 389 type=190 (LJ14) 147 150
39: 390 type=190 (LJ14) 147 154
39: 391 type=193 (LJ14) 149 151
39: 392 type=193 (LJ14) 149 152
39: 393 type=193 (LJ14) 149 153
39: 394 type=194 (LJ14) 149 155
39: 395 type=195 (LJ14) 150 155
39: 396 type=196 (LJ14) 151 154
39: 397 type=196 (LJ14) 152 154
39: 398 type=196 (LJ14) 153 154
39: Coulomb-14:
39: nr: 0
39: LJC-14 q:
39: nr: 0
39: LJC Pairs NB:
39: nr: 0
39: LJ (SR):
39: nr: 0
39: Buck.ham (SR):
39: nr: 0
39: LJ (unused):
39: nr: 0
39: B.ham (unused):
39: nr: 0
39: Disper. corr.:
39: nr: 0
39: Coulomb (SR):
39: nr: 0
39: Coul (unused):
39: nr: 0
39: RF excl.:
39: nr: 0
39: Coul. recip.:
39: nr: 0
39: LJ recip.:
39: nr: 0
39: DPD:
39: nr: 0
39: Polarization:
39: nr: 0
39: Water Pol.:
39: nr: 0
39: Thole Pol.:
39: nr: 0
39: Anharm. Pol.:
39: nr: 0
39: Position Rest.:
39: nr: 0
39: Flat-bottom posres:
39: nr: 0
39: Dis. Rest.:
39: nr: 0
39: D.R.Viol. (nm):
39: nr: 0
39: Orient. Rest.:
39: nr: 0
39: Ori. R. RMSD:
39: nr: 0
39: Angle Rest.:
39: nr: 0
39: Angle Rest. Z:
39: nr: 0
39: Dih. Rest.:
39: nr: 0
39: Dih. Rest. Viol.:
39: nr: 0
39: Constraint:
39: nr: 0
39: Constr. No Conn.:
39: nr: 0
39: Settle:
39: nr: 0
39: Virtual site 2:
39: nr: 0
39: Virtual site 2fd:
39: nr: 0
39: Virtual site 3:
39: nr: 0
39: Virtual site 3fd:
39: nr: 0
39: Virtual site 3fad:
39: nr: 0
39: Virtual site 3out:
39: nr: 0
39: Virtual site 4fd:
39: nr: 0
39: Virtual site 4fdn:
39: nr: 0
39: Virtual site N:
39: nr: 0
39: COM Pull En.:
39: nr: 0
39: Density fitting:
39: nr: 0
39: Quantum En.:
39: nr: 0
39: Potential:
39: nr: 0
39: Kinetic En.:
39: nr: 0
39: Total Energy:
39: nr: 0
39: Conserved En.:
39: nr: 0
39: Temperature:
39: nr: 0
39: Vir. Temp. (not used):
39: nr: 0
39: Pres. DC:
39: nr: 0
39: Pressure:
39: nr: 0
39: dH/dl constr.:
39: nr: 0
39: dVremain/dl:
39: nr: 0
39: dEkin/dl:
39: nr: 0
39: dVcoul/dl:
39: nr: 0
39: dVvdw/dl:
39: nr: 0
39: dVbonded/dl:
39: nr: 0
39: dVrestraint/dl:
39: nr: 0
39: dVtemperature/dl:
39: nr: 0
39: grp[T-Coupling ] nr=1, name=[ rest]
39: grp[Energy Mon. ] nr=1, name=[ rest]
39: grp[Acceleration] nr=1, name=[ rest]
39: grp[Freeze ] nr=1, name=[ rest]
39: grp[User1 ] nr=1, name=[ rest]
39: grp[User2 ] nr=1, name=[ rest]
39: grp[VCM ] nr=1, name=[ rest]
39: grp[Compressed X] nr=1, name=[ rest]
39: grp[Or. Res. Fit] nr=1, name=[ rest]
39: grp[QMMM ] nr=1, name=[ rest]
39: grpname (11):
39: grpname[0]={name="System"}
39: grpname[1]={name="Protein"}
39: grpname[2]={name="Protein-H"}
39: grpname[3]={name="C-alpha"}
39: grpname[4]={name="Backbone"}
39: grpname[5]={name="MainChain"}
39: grpname[6]={name="MainChain+Cb"}
39: grpname[7]={name="MainChain+H"}
39: grpname[8]={name="SideChain"}
39: grpname[9]={name="SideChain-H"}
39: grpname[10]={name="rest"}
39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
39: allocated 0 0 0 0 0 0 0 0 0 0
39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
39: box (3x3):
39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
39: box_rel (3x3):
39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv (3x3):
39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev (3x3):
39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev (3x3):
39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev (3x3):
39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: nosehoover_xi: not available
39: x (156x3):
39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
39: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
39: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
39: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
39: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
39: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
39: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
39: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
39: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
39: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
39: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
39: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
39: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
39: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
39: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
39: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
39: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
39: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
39: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
39: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
39: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
39: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
39: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
39: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
39: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
39: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
39: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
39: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
39: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
39: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
39: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
39: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
39: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
39: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
39: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
39: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
39: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
39: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
39: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
39: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
39: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
39: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
39: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
39: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
39: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
39: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
39: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
39: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
39: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
39: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
39: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
39: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
39: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
39: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
39: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
39: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
39: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
39: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
39: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
39: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
39: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
39: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
39: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
39: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
39: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
39: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
39: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
39: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
39: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
39: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
39: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
39: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
39: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
39: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
39: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
39: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
39: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
39: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
39: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
39: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
39: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
39: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
39: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
39: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
39: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
39: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
39: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
39: v (156x3):
39: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: Group statistics
39: T-Coupling : 156 (total 156 atoms)
39: Energy Mon. : 156 (total 156 atoms)
39: Acceleration: 156 (total 156 atoms)
39: Freeze : 156 (total 156 atoms)
39: User1 : 156 (total 156 atoms)
39: User2 : 156 (total 156 atoms)
39: VCM : 156 (total 156 atoms)
39: Compressed X: 156 (total 156 atoms)
39: Or. Res. Fit: 156 (total 156 atoms)
39: QMMM : 156 (total 156 atoms)
39: [ OK ] DumpTest.WorksWithTpr (55 ms)
39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (7 ms)
39: [----------] 2 tests from DumpTest (62 ms total)
39:
39: [----------] 4 tests from ReportMethodsTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -604522635
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (1 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectInformation
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
39: [ OK ] ReportMethodsTest.WritesCorrectInformation (4 ms)
39: [ RUN ] ReportMethodsTest.ToolEndToEndTest
39: Reading file /<<PKGBUILDDIR>>/build/basic/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
39: section: Methods
39: subsection: Simulation system
39: A system of 1 molecules (156 atoms) was simulated.
39:
39: subsection: Simulation settings
39: A total of 0 ns were simulated with a time step of 1 fs.
39: Neighbor searching was performed every 10 steps.
39: The Cut-off algorithm was used for electrostatic interactions.
39: with a cut-off of 1 nm.
39: A single cut-off of 1.1 nm was used for Van der Waals interactions.
39: [ OK ] ReportMethodsTest.ToolEndToEndTest (5 ms)
39: [----------] 4 tests from ReportMethodsTest (11 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: trr version: GMX_trn_file (single precision)
39:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (16 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (14 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (13 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (14 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (13 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (13 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (85 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (5 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (4 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (25 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 18 tests from 4 test cases ran. (7680 ms total)
39: [ PASSED ] 18 tests.
39/54 Test #39: ToolUnitTests ....................... Passed 7.76 sec
test 40
Start 40: FileIOTests
40: Test command: /<<PKGBUILDDIR>>/build/basic/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/FileIOTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 33 tests from 8 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from FileMD5Test
40: [ RUN ] FileMD5Test.CanComputeMD5
40: [ OK ] FileMD5Test.CanComputeMD5 (4 ms)
40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
40: [----------] 2 tests from FileMD5Test (6 ms total)
40:
40: [----------] 3 tests from MrcSerializer
40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (4 ms)
40: [----------] 3 tests from MrcSerializer (4 ms total)
40:
40: [----------] 4 tests from MrcDensityMap
40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (4 ms)
40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (1 ms)
40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms)
40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (20 ms)
40: [----------] 4 tests from MrcDensityMap (28 ms total)
40:
40: [----------] 8 tests from MrcDensityMapHeaderTest
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (1 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.IsSane
40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
40: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
40:
40: [----------] 9 tests from ReadTest
40: [ RUN ] ReadTest.get_eint_ReadsInteger
40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_eint64_ReadsInteger
40: [ OK ] ReadTest.get_eint64_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (1 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsInteger
40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsFloat
40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
40: [ RUN ] ReadTest.get_ereal_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not a
40: real value
40:
40:
40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
40: [----------] 9 tests from ReadTest (1 ms total)
40:
40: [----------] 1 test from FileIOXdrSerializerTest
40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms)
40: [----------] 1 test from FileIOXdrSerializerTest (1 ms total)
40:
40: [----------] 2 tests from TngTest
40: [ RUN ] TngTest.CanOpenTngFile
40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
40: [ OK ] TngTest.CanOpenTngFile (1 ms)
40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
40: [----------] 2 tests from TngTest (1 ms total)
40:
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (9 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (3 ms)
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (18 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 33 tests from 8 test cases ran. (60 ms total)
40: [ PASSED ] 33 tests.
40/54 Test #40: FileIOTests ......................... Passed 0.13 sec
test 41
Start 41: SelectionUnitTests
41: Test command: /<<PKGBUILDDIR>>/build/basic/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/SelectionUnitTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 192 tests from 11 test cases.
41: [----------] Global test environment set-up.
41: [----------] 1 test from IndexGroupTest
41: [ RUN ] IndexGroupTest.RemovesDuplicates
41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
41: [----------] 1 test from IndexGroupTest (1 ms total)
41:
41: [----------] 15 tests from IndexBlockTest
41: [ RUN ] IndexBlockTest.CreatesUnknownBlock
41: [ OK ] IndexBlockTest.CreatesUnknownBlock (27 ms)
41: [ RUN ] IndexBlockTest.CreatesAtomBlock
41: [ OK ] IndexBlockTest.CreatesAtomBlock (9 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (20 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (3 ms)
41: [ RUN ] IndexBlockTest.CreatesSingleBlock
41: [ OK ] IndexBlockTest.CreatesSingleBlock (3 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (1 ms)
41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (1 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
41: [----------] 15 tests from IndexBlockTest (70 ms total)
41:
41: [----------] 11 tests from IndexMapTest
41: [ RUN ] IndexMapTest.InitializesAtomBlock
41: [ OK ] IndexMapTest.InitializesAtomBlock (1 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (13 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (5 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (5 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (3 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (3 ms)
41: [ RUN ] IndexMapTest.InitializesMoleculeBlock
41: [ OK ] IndexMapTest.InitializesMoleculeBlock (1 ms)
41: [ RUN ] IndexMapTest.MapsSingleBlock
41: [ OK ] IndexMapTest.MapsSingleBlock (4 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocks
41: [ OK ] IndexMapTest.MapsResidueBlocks (17 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (11 ms)
41: [ RUN ] IndexMapTest.HandlesMultipleRequests
41: [ OK ] IndexMapTest.HandlesMultipleRequests (22 ms)
41: [----------] 11 tests from IndexMapTest (88 ms total)
41:
41: [----------] 3 tests from IndexGroupsAndNamesTest
41: [ RUN ] IndexGroupsAndNamesTest.containsNames
41: [ OK ] IndexGroupsAndNamesTest.containsNames (0 ms)
41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (3 ms)
41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
41: [----------] 3 tests from IndexGroupsAndNamesTest (3 ms total)
41:
41: [----------] 15 tests from NeighborhoodSearchTest
41: [ RUN ] NeighborhoodSearchTest.SimpleSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSearch (101 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (79 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchBox
41: [ OK ] NeighborhoodSearchTest.GridSearchBox (12 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (45 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (23 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (11 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (13 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (1 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (196 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (17 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (4 ms)
41: [----------] 15 tests from NeighborhoodSearchTest (503 ms total)
41:
41: [----------] 12 tests from PositionCalculationTest
41: [ RUN ] PositionCalculationTest.ComputesAtomPositions
41: [ OK ] PositionCalculationTest.ComputesAtomPositions (6 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (3 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (3 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (2 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (2 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (3 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionMask
41: [ OK ] PositionCalculationTest.ComputesPositionMask (2 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (2 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (2 ms)
41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (3 ms)
41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (2 ms)
41: [----------] 12 tests from PositionCalculationTest (32 ms total)
41:
41: [----------] 29 tests from SelectionCollectionTest
41: [ RUN ] SelectionCollectionTest.HandlesNoSelections
41: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (3 ms)
41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (1 ms)
41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (3 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (3 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (3 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (3 ms)
41: [----------] 29 tests from SelectionCollectionTest (53 ms total)
41:
41: [----------] 14 tests from SelectionCollectionInteractiveTest
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (4 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (2 ms)
41: [----------] 14 tests from SelectionCollectionInteractiveTest (40 ms total)
41:
41: [----------] 66 tests from SelectionCollectionDataTest
41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResnr
41: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesChain
41: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMass
41: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCharge
41: [ OK ] SelectionCollectionDataTest.HandlesCharge (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBeta
41: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResname
41: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (27 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (12 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (12 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (12 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (10 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (7 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms)
41: [----------] 66 tests from SelectionCollectionDataTest (351 ms total)
41:
41: [----------] 17 tests from SelectionOptionTest
41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (2 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (3 ms)
41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptySelections
41: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelections
41: [ OK ] SelectionOptionTest.HandlesTooManySelections (2 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesAdjuster
41: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (2 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
41: [----------] 17 tests from SelectionOptionTest (23 ms total)
41:
41: [----------] 9 tests from SelectionFileOptionTest
41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (2 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (2 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (2 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (1 ms)
41: [----------] 9 tests from SelectionFileOptionTest (13 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 192 tests from 11 test cases ran. (1178 ms total)
41: [ PASSED ] 192 tests.
41/54 Test #41: SelectionUnitTests .................. Passed 1.27 sec
test 42
Start 42: MdrunOutputTests
42: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunOutputTests.xml"
42: Test timeout computed to be: 600
42: [==========] Running 12 tests from 5 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from MdrunTest
42: [ RUN ] MdrunTest.WritesHelp
42: [ OK ] MdrunTest.WritesHelp (58 ms)
42: [----------] 1 test from MdrunTest (58 ms total)
42:
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
42: Setting the LD random seed to -402653411
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.470 0.235 199.7
42: (ns/day) (hour/ns)
42: Performance: 0.734 32.697
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (349 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
42: Setting the LD random seed to -1162348582
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.439 0.220 199.8
42: (ns/day) (hour/ns)
42: Performance: 0.787 30.488
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (276 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
42: Setting the LD random seed to 796720946
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.408 0.204 199.8
42: (ns/day) (hour/ns)
42: Performance: 0.847 28.342
42:
Reading frame 0 time 0.000
42: # Atoms 3
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (246 ms)
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (874 ms total)
42:
42: [----------] 2 tests from Argon12/OutputFiles
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.433 0.217 199.8
42: (ns/day) (hour/ns)
42: Performance: 6.782 3.539
42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (263 ms)
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.370 0.185 199.8
42: (ns/day) (hour/ns)
42: Performance: 7.934 3.025
42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (222 ms)
42: [----------] 2 tests from Argon12/OutputFiles (487 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/Trajectories
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
42: Setting the LD random seed to -1359010818
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.332 0.166 199.7
42: (ns/day) (hour/ns)
42: Performance: 3.637 6.599
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (212 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
42: Setting the LD random seed to -193004053
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.330 0.165 199.7
42: (ns/day) (hour/ns)
42: Performance: 3.656 6.564
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (210 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
42: Setting the LD random seed to -16784103
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.333 0.167 199.7
42: (ns/day) (hour/ns)
42: Performance: 3.621 6.628
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (210 ms)
42: [----------] 3 tests from MdrunCanWrite/Trajectories (634 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
42: Setting the LD random seed to -139759809
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.267 0.134 199.6
42: (ns/day) (hour/ns)
42: Performance: 1.939 12.377
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (177 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
42: Setting the LD random seed to -541102337
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.268 0.134 199.6
42: (ns/day) (hour/ns)
42: Performance: 1.928 12.448
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (177 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
42: Setting the LD random seed to -151263273
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42:
42: Non-default thread affinity set, disabling internal thread affinity
42:
42: Using 2 OpenMP threads
42:
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.269 0.135 199.5
42: (ns/day) (hour/ns)
42: Performance: 1.925 12.468
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (177 ms)
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (533 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 12 tests from 5 test cases ran. (2587 ms total)
42: [ PASSED ] 12 tests.
42/54 Test #42: MdrunOutputTests .................... Passed 2.65 sec
test 43
Start 43: MdrunModulesTests
43: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunModulesTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 10 tests from 3 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to -136487687
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.8565400e+03
43: Maximum force = 2.8846870e+03 on atom 3
43: Norm of force = 1.0754448e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (84 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to 1828048319
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.7138666e+04
43: Maximum force = 4.3409717e+03 on atom 2
43: Norm of force = 1.2549793e+03
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (42 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (37 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to -537670675
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.336 0.168 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.542 15.569
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.328 0.164 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.627 9.136
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (385 ms)
43: [----------] 4 tests from DensityFittingTest (550 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1454374901
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 188.6
43: (ns/day) (hour/ns)
43: Performance: 46.082 0.521
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (41 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1204696525
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.004 0.002 188.4
43: (ns/day) (hour/ns)
43: Performance: 45.681 0.525
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (40 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 2147351999
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.002 182.6
43: (ns/day) (hour/ns)
43: Performance: 47.954 0.500
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (38 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to 1505736925
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.006 0.003 191.7
43: (ns/day) (hour/ns)
43: Performance: 28.697 0.836
43: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (197 ms)
43: [----------] 4 tests from MimicTest (317 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to -1430892545
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 53789.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.491 0.246 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.110 11.376
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (1314 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to -71843937
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 52677.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.1977063e+03
43: Maximum force = 1.7794877e+04 on atom 9
43: Norm of force = 7.8732901e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (1056 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (2370 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 10 tests from 3 test cases ran. (3238 ms total)
43: [ PASSED ] 10 tests.
43/54 Test #43: MdrunModulesTests ................... Passed 3.31 sec
test 44
Start 44: MdrunIOTests
44: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunIOTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 51 tests from 9 test cases.
44: [----------] Global test environment set-up.
44: [----------] 3 tests from GromppTest
44: [ RUN ] GromppTest.EmptyMdpFileWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -38290497
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.EmptyMdpFileWorks (27 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to 1736272943
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group rest: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorks (24 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -1768226849
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group Methanol: Single, 3 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 3.0 280.0
44: 6.0- 270.0
44: Simulated annealing for group SOL: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group Methanol is 7.20
44: Number of degrees of freedom in T-Coupling group SOL is 4.80
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (25 ms)
44: [----------] 3 tests from GromppTest (79 ms total)
44:
44: [----------] 6 tests from MdrunTerminationTest
44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
44: Setting the LD random seed to -1073742977
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.379 0.190 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.366 17.576
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.315 0.157 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.646 14.583
44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (445 ms)
44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
44: Setting the LD random seed to 1525283551
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 1, rlist from 1.024 to 1
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 100 steps, 0.1 ps.
44:
44: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.366 0.183 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.414 16.979
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Setting nsteps to 102
44: Writing statusfile with starting step 0 and length 102 steps...
44: time 0.000 and length 0.102 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.356 0.179 199.7
44: (ns/day) (hour/ns)
44: Performance: 48.885 0.491
44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (425 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
44: Setting the LD random seed to -69206113
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.307 0.154 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.685 14.246
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.286 0.143 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.814 13.233
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Setting nsteps to 6
44: Writing statusfile with starting step 0 and length 6 steps...
44: time 0.000 and length 0.006 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.330 0.165 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.571 15.280
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Setting nsteps to 8
44: Writing statusfile with starting step 0 and length 8 steps...
44: time 0.000 and length 0.008 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.261 0.131 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.983 12.102
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.001 0.001 166.2
44: (ns/day) (hour/ns)
44: Performance: 119.758 0.200
44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (711 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
44: Setting the LD random seed to -17319121
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.299 0.150 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.732 13.856
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.284 0.142 199.4
44: (ns/day) (hour/ns)
44: Performance: 3.032 7.914
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (341 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
44: Setting the LD random seed to 2147219143
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.327 0.164 199.6
44: (ns/day) (hour/ns)
44: Performance: 1.581 15.183
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (203 ms)
44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
44: Setting the LD random seed to -378535941
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.320 0.160 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.617 14.847
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.321 0.160 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.616 14.855
44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (375 ms)
44: [----------] 6 tests from MdrunTerminationTest (2501 ms total)
44:
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.476 0.238 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.166 3.892
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.428 0.214 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.629 6.613
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.396 0.198 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.923 6.118
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (737 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.485 0.243 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.055 3.964
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.403 0.204 197.9
44: (ns/day) (hour/ns)
44: Performance: 3.820 6.283
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.368 0.184 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.227 5.678
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (710 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.388 0.194 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.567 3.172
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.335 0.168 199.6
44: (ns/day) (hour/ns)
44: Performance: 4.629 5.185
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.334 0.167 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.644 5.168
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (611 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.500 0.250 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.869 4.089
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.440 0.220 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.532 6.794
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.408 0.204 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.805 6.308
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (766 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.473 0.237 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.208 3.866
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.447 0.224 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.476 6.905
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.379 0.190 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.103 5.850
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (733 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.373 0.187 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.871 3.049
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.360 0.180 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.315 5.562
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.145 0.573 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.357 17.680
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (1034 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.327 0.164 199.7
44: (ns/day) (hour/ns)
44: Performance: 8.968 2.676
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.461 0.231 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.368 7.127
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.171 0.586 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.327 18.087
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (1078 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.148 0.574 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.557 9.387
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.419 0.210 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.708 6.473
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.422 0.211 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.682 6.519
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (1097 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.465 0.233 199.7
44: (ns/day) (hour/ns)
44: Performance: 6.306 3.806
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.483 0.242 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.217 7.461
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.461 0.231 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.368 7.126
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (1013 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.517 0.259 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.678 4.227
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.460 0.231 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.369 7.124
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.458 0.729 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.066 22.514
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (1589 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.483 0.242 199.6
44: (ns/day) (hour/ns)
44: Performance: 6.072 3.953
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.390 0.196 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.973 6.040
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.502 0.251 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.092 7.762
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1144 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.069 0.535 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.747 8.737
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.541 0.771 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.009 23.793
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.471 0.736 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.056 22.718
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (2411 ms)
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (12926 ms total)
44:
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.560 0.280 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.239 4.581
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.520 0.261 199.3
44: (ns/day) (hour/ns)
44: Performance: 2.979 8.057
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.567 0.284 199.7
44: (ns/day) (hour/ns)
44: Performance: 2.736 8.770
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1532 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.621 0.311 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.727 5.077
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.500 0.250 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.111 7.714
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.588 0.294 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.641 9.087
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1134 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.725 0.363 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.047 5.930
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.535 0.268 199.3
44: (ns/day) (hour/ns)
44: Performance: 2.896 8.286
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.517 0.259 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.003 7.991
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1376 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.684 0.342 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.291 5.593
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.540 0.271 199.4
44: (ns/day) (hour/ns)
44: Performance: 2.871 8.361
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.573 0.287 199.7
44: (ns/day) (hour/ns)
44: Performance: 2.708 8.864
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1278 ms)
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (5321 ms total)
44:
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.450 0.225 199.7
44: (ns/day) (hour/ns)
44: Performance: 6.519 3.681
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.451 0.226 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.442 6.972
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.352 0.176 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.415 5.437
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (711 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.461 0.231 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.365 3.771
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.447 0.224 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.477 6.902
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.379 0.190 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.097 5.858
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (731 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.411 0.206 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.142 3.360
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.380 0.190 199.6
44: (ns/day) (hour/ns)
44: Performance: 4.087 5.872
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.353 0.177 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.399 5.456
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (656 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.413 0.207 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.103 3.379
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.397 0.199 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.909 6.140
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.575 0.288 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.703 8.880
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (802 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 2.765 1.383 200.0
44: (ns/day) (hour/ns)
44: Performance: 1.062 22.592
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.412 0.206 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.773 6.361
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.419 0.210 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.708 6.473
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (1887 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.404 0.202 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.269 3.302
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.358 0.179 199.6
44: (ns/day) (hour/ns)
44: Performance: 4.339 5.531
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.335 0.168 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.640 5.173
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (654 ms)
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (5442 ms total)
44:
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.388 0.194 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.566 3.172
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.475 0.238 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.264 7.352
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.927 0.464 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.676 14.321
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (978 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.943 0.472 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.113 7.709
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.026 0.514 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.514 15.850
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.133 0.567 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.372 17.497
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1634 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.365 0.183 199.7
44: (ns/day) (hour/ns)
44: Performance: 8.041 2.985
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.335 0.168 199.4
44: (ns/day) (hour/ns)
44: Performance: 4.623 5.192
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.538 0.269 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.888 8.309
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (701 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.019 0.510 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.882 8.328
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.422 0.711 200.0
44: (ns/day) (hour/ns)
44: Performance: 1.093 21.949
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.398 0.699 200.0
44: (ns/day) (hour/ns)
44: Performance: 1.112 21.573
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (2012 ms)
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (5325 ms total)
44:
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.526 0.263 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.584 4.298
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.421 0.211 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.681 6.519
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.374 0.187 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.154 5.778
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (758 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.459 0.230 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.388 3.757
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.419 0.210 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.703 6.482
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.396 0.198 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.920 6.122
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (752 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.465 0.233 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.306 3.806
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.441 0.221 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.517 6.823
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.382 0.192 198.8
44: (ns/day) (hour/ns)
44: Performance: 4.047 5.931
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (735 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.390 0.195 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.528 3.188
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.335 0.168 199.4
44: (ns/day) (hour/ns)
44: Performance: 4.629 5.185
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.311 0.156 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.993 4.807
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (607 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.408 0.204 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.199 3.334
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.402 0.202 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.858 6.221
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.401 0.201 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.876 6.192
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (689 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.497 0.249 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.899 4.069
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.424 0.213 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.658 6.562
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.423 0.212 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.668 6.543
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (755 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.453 0.227 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.479 3.704
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.358 0.180 199.4
44: (ns/day) (hour/ns)
44: Performance: 4.330 5.543
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.334 0.167 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.654 5.157
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (656 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.585 0.293 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.020 4.781
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.434 0.217 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.580 6.705
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.418 0.210 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.712 6.466
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (811 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.470 0.235 199.9
44: (ns/day) (hour/ns)
44: Performance: 6.249 3.840
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.434 0.217 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.578 6.708
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.417 0.209 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.726 6.441
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (765 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1 ms)
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (6531 ms total)
44:
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.543 0.772 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.903 12.614
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.021 0.511 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.523 15.762
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.312 0.156 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.982 4.818
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as single precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1521 ms)
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (1521 ms total)
44:
44: [----------] 3 tests from Checking/InitialConstraintsTest
44: [ RUN ] Checking/InitialConstraintsTest.Works/0
44: Setting the LD random seed to -1111500915
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.316 0.158 199.6
44: (ns/day) (hour/ns)
44: Performance: 1.091 21.998
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (195 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/1
44: Setting the LD random seed to -37798593
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.305 0.152 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.133 21.176
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (190 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: Integrator method md-vv-avek is implemented primarily for validation
44: purposes; for molecular dynamics, you should probably be using md or md-vv
44:
44: Setting the LD random seed to -271581185
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.364 0.182 199.7
44: (ns/day) (hour/ns)
44: Performance: 0.948 25.311
44: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as single precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (222 ms)
44: [----------] 3 tests from Checking/InitialConstraintsTest (608 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 51 tests from 9 test cases ran. (40257 ms total)
44: [ PASSED ] 51 tests.
44/54 Test #44: MdrunIOTests ........................ Passed 40.34 sec
test 45
Start 45: MdrunTests
45: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 12 tests from 5 test cases.
45: [----------] Global test environment set-up.
45: [----------] 1 test from DispersionCorrectionTest
45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to -1115693169
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
45: Cleaning up constraints and constant bonded interactions with virtual sites
45: Converted 3 Bonds with virtual sites to connections, 7 left
45: Removed 18 Angles with virtual sites, 21 left
45: Removed 10 Proper Dih.s with virtual sites, 44 left
45: Converted 12 Constraints with virtual sites to connections, 0 left
45: Number of degrees of freedom in T-Coupling group System is 30.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: There are 9 non-linear virtual site constructions. Their contribution to
45: the energy error is approximated. In most cases this does not affect the
45: error significantly.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Changing nstlist from 10 to 50, rlist from 1.016 to 1.167
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Alanine dipeptide in vacuo'
45: 200 steps, 0.4 ps.
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.607 0.304 199.8
45: (ns/day) (hour/ns)
45: Performance: 114.308 0.210
45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (598 ms)
45: [----------] 1 test from DispersionCorrectionTest (598 ms total)
45:
45: [----------] 1 test from OriresTest
45: [ RUN ] OriresTest.OriresCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 1538916350
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 518.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
45: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
45:
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
45: 10 steps, 0.0 ps.
45: turning H bonds into constraints...
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.487 0.244 199.7
45: (ns/day) (hour/ns)
45: Performance: 7.799 3.077
45: [ OK ] OriresTest.OriresCanRun (1945 ms)
45: [----------] 1 test from OriresTest (1945 ms total)
45:
45: [----------] 3 tests from PmeTest
45: [ RUN ] PmeTest.ReproducesEnergies
45: Setting the LD random seed to -269017173
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.593 0.297 199.8
45: (ns/day) (hour/ns)
45: Performance: 6.112 3.927
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.648 0.324 199.8
45: (ns/day) (hour/ns)
45: Performance: 5.599 4.287
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45:
45: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.584 0.292 199.8
45: (ns/day) (hour/ns)
45: Performance: 6.209 3.865
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (11868 ms)
45: [ RUN ] PmeTest.ScalesTheBox
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -142780417
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.012 0.006 190.3
45: (ns/day) (hour/ns)
45: Performance: 13.940 1.722
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBox (72 ms)
45: [ RUN ] PmeTest.ScalesTheBoxWithWalls
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 468966783
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Searching the wall atom type(s)
45: Number of degrees of freedom in T-Coupling group rest is 13.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: NVE simulation: will use the initial temperature of 966.268 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.048 0.024 196.8
45: (ns/day) (hour/ns)
45: Performance: 3.528 6.803
45: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBoxWithWalls (33675 ms)
45: [----------] 3 tests from PmeTest (45617 ms total)
45:
45: [----------] 1 test from CompelTest
45: [ RUN ] CompelTest.SwapCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 2012839791
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 1 bonded neighbours molecule type 'NA'
45: Excluding 1 bonded neighbours molecule type 'CL'
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Split0 group 'Ch0' contains 83 atoms.
45: Split1 group 'Ch1' contains 83 atoms.
45: Solvent group 'SOL' contains 11931 atoms.
45: Swap group 'NA+' contains 19 atoms.
45: Swap group 'CL-' contains 19 atoms.
45: Number of degrees of freedom in T-Coupling group System is 27869.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: Removing center of mass motion in the presence of position restraints
45: might cause artifacts. When you are using position restraints to
45: equilibrate a macro-molecule, the artifacts are usually negligible.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: Non-default thread affinity set probably by the OpenMP library,
45: disabling internal thread affinity
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Determining initial numbers of ions per compartment.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 2 steps, 0.0 ps.
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 1 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 5.501 2.751 200.0
45: (ns/day) (hour/ns)
45: Performance: 0.471 50.939
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
45:
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Copying channel fluxes from checkpoint file data
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 5.029 2.515 200.0
45: (ns/day) (hour/ns)
45: Performance: 0.515 46.573
45: [ OK ] CompelTest.SwapCanRun (10453 ms)
45: [----------] 1 test from CompelTest (10453 ms total)
45:
45: [----------] 6 tests from BondedInteractionsTest
45: [ RUN ] BondedInteractionsTest.NormalBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -336101381
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.001 186.9
45: (ns/day) (hour/ns)
45: Performance: 58.131 0.413
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalBondWorks (44 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1071626103
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 185.4
45: (ns/day) (hour/ns)
45: Performance: 54.708 0.439
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (48 ms)
45: [ RUN ] BondedInteractionsTest.NormalAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 494387197
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 187.6
45: (ns/day) (hour/ns)
45: Performance: 52.780 0.455
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalAngleWorks (40 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -169345241
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 185.2
45: (ns/day) (hour/ns)
45: Performance: 53.895 0.445
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (42 ms)
45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -67372033
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 185.6
45: (ns/day) (hour/ns)
45: Performance: 54.750 0.438
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (35 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1122250857
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45:
45: Non-default thread affinity set, disabling internal thread affinity
45:
45: Using 2 OpenMP threads
45:
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 185.9
45: (ns/day) (hour/ns)
45: Performance: 51.192 0.469
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (42 ms)
45: [----------] 6 tests from BondedInteractionsTest (252 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 12 tests from 5 test cases ran. (58869 ms total)
45: [ PASSED ] 12 tests.
45:
45: YOU HAVE 12 DISABLED TESTS
45:
45/54 Test #45: MdrunTests .......................... Passed 58.96 sec
test 46
Start 46: MdrunNonIntegratorTests
46: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunNonIntegratorTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 58 tests from 5 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from NonbondedBenchTest
46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
46: System size: 3000 atoms
46: Cut-off radius: 1 nm
46: Number of threads: 1
46: Number of iterations: 1
46: Compute energies: no
46: Ewald excl. corr.: analytical
46:
46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
46: total useful
46: Ewald all geom. no 0.000 0.0000 inf inf
46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (564 ms)
46: [----------] 1 test from NonbondedBenchTest (565 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.7990990e+01
46: Maximum force = 1.8629828e+02 on atom 13
46: Norm of force = 8.7721844e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (3269 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.5862099e+01
46: Maximum force = 4.2728845e+02 on atom 13
46: Norm of force = 1.8453478e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (3301 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1937714e+02
46: Maximum force = 9.9988643e+03 on atom 9
46: Norm of force = 4.6166996e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1042 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5174377e+02
46: Maximum force = 7.4208838e+03 on atom 9
46: Norm of force = 3.5693005e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1064 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.5698413e+02
46: Maximum force = 4.5704984e+02 on atom 17
46: Norm of force = 1.8327747e+02
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (116 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06801e+03 on atom 28
46: F-Norm = 4.26916e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.6941180e+02
46: Maximum force = 2.1832491e+02 on atom 17
46: Norm of force = 7.9220732e+01
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (116 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (8909 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.7425699e-01
46: Maximum force = 4.0132303e+00 on atom 1
46: Norm of force = 1.6383944e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (36 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.9064207e-01
46: Maximum force = 2.5781622e+00 on atom 1
46: Norm of force = 1.0525302e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (37 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.9064207e-01
46: Maximum force = 2.5781622e+00 on atom 1
46: Norm of force = 1.0525302e+00
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (37 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.1939697e+02
46: Maximum force = 9.9704248e+03 on atom 9
46: Norm of force = 4.6227540e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1060 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.5625757e+02
46: Maximum force = 7.5018242e+03 on atom 9
46: Norm of force = 3.6139019e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1058 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 5.6111725e+02
46: Maximum force = 1.2685491e+04 on atom 10
46: Norm of force = 6.0643622e+03
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1060 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3288 ms total)
46:
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 1.053 0.527 199.9
46: (ns/day) (hour/ns)
46: Performance: 2.787 8.610
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
46:
46: trr version: GMX_trn_file (single precision)
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.9
46: (ns/day) (hour/ns)
46: Performance: 402.785 0.060
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (587 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.406 0.203 199.9
46: (ns/day) (hour/ns)
46: Performance: 7.237 3.316
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.006 0.003 193.3
46: (ns/day) (hour/ns)
46: Performance: 441.936 0.054
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (263 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.343 0.172 199.7
46: (ns/day) (hour/ns)
46: Performance: 8.541 2.810
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.003 193.6
46: (ns/day) (hour/ns)
46: Performance: 427.226 0.056
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (233 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.388 0.194 199.8
46: (ns/day) (hour/ns)
46: Performance: 7.557 3.176
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.003 193.6
46: (ns/day) (hour/ns)
46: Performance: 423.554 0.057
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (256 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.488 0.244 199.8
46: (ns/day) (hour/ns)
46: Performance: 6.013 3.991
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.5
46: (ns/day) (hour/ns)
46: Performance: 402.128 0.060
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (3580 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.468 0.234 199.9
46: (ns/day) (hour/ns)
46: Performance: 6.272 3.827
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.3
46: (ns/day) (hour/ns)
46: Performance: 408.419 0.059
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (3567 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.479 0.240 199.8
46: (ns/day) (hour/ns)
46: Performance: 6.127 3.917
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.8
46: (ns/day) (hour/ns)
46: Performance: 392.345 0.061
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (3567 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.497 0.249 199.8
46: (ns/day) (hour/ns)
46: Performance: 5.909 4.062
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.6
46: (ns/day) (hour/ns)
46: Performance: 395.645 0.061
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (3578 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.461 0.231 199.6
46: (ns/day) (hour/ns)
46: Performance: 6.363 3.772
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.011 0.006 194.5
46: (ns/day) (hour/ns)
46: Performance: 250.522 0.096
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (395 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.460 0.230 199.7
46: (ns/day) (hour/ns)
46: Performance: 6.379 3.763
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.011 0.006 192.6
46: (ns/day) (hour/ns)
46: Performance: 248.812 0.096
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (388 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.433 0.217 199.7
46: (ns/day) (hour/ns)
46: Performance: 6.768 3.546
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 194.3
46: (ns/day) (hour/ns)
46: Performance: 247.274 0.097
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (491 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.514 0.257 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.709 4.204
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.012 0.006 194.7
46: (ns/day) (hour/ns)
46: Performance: 244.847 0.098
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (491 ms)
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (17399 ms total)
46:
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.529 0.265 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.544 4.329
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.008 186.1
46: (ns/day) (hour/ns)
46: Performance: 191.091 0.126
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (421 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.580 0.290 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.057 4.746
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.008 189.0
46: (ns/day) (hour/ns)
46: Performance: 193.468 0.124
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (445 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.529 0.265 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.543 4.330
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.008 187.5
46: (ns/day) (hour/ns)
46: Performance: 192.218 0.125
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (421 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.487 0.244 199.7
46: (ns/day) (hour/ns)
46: Performance: 6.018 3.988
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.008 187.5
46: (ns/day) (hour/ns)
46: Performance: 192.422 0.125
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (399 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.575 0.288 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.098 4.708
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 188.7
46: (ns/day) (hour/ns)
46: Performance: 185.941 0.129
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (444 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.606 0.303 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.843 4.955
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 186.9
46: (ns/day) (hour/ns)
46: Performance: 197.544 0.121
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (451 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.568 0.285 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.161 4.650
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 184.4
46: (ns/day) (hour/ns)
46: Performance: 197.183 0.122
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (434 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.825 0.413 199.8
46: (ns/day) (hour/ns)
46: Performance: 3.558 6.745
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.016 0.009 188.7
46: (ns/day) (hour/ns)
46: Performance: 168.304 0.143
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (627 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.491 0.246 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.969 4.021
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 187.1
46: (ns/day) (hour/ns)
46: Performance: 201.987 0.119
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (394 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.502 0.251 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.846 4.106
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 187.1
46: (ns/day) (hour/ns)
46: Performance: 202.166 0.119
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (400 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.606 0.303 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.844 4.955
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 186.8
46: (ns/day) (hour/ns)
46: Performance: 205.257 0.117
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (452 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.579 0.290 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.073 4.731
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 187.0
46: (ns/day) (hour/ns)
46: Performance: 204.528 0.117
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (438 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.589 0.295 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.985 4.814
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 187.0
46: (ns/day) (hour/ns)
46: Performance: 201.518 0.119
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (445 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.549 0.275 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.348 4.487
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 189.4
46: (ns/day) (hour/ns)
46: Performance: 181.327 0.132
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (441 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.556 0.278 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.278 4.547
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 186.9
46: (ns/day) (hour/ns)
46: Performance: 204.413 0.117
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (435 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.523 0.262 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.614 4.275
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 185.1
46: (ns/day) (hour/ns)
46: Performance: 202.751 0.118
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (411 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.500 0.250 199.8
46: (ns/day) (hour/ns)
46: Performance: 5.868 4.090
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 186.9
46: (ns/day) (hour/ns)
46: Performance: 200.658 0.120
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (401 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.587 0.294 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.003 4.797
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 185.4
46: (ns/day) (hour/ns)
46: Performance: 202.831 0.118
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (443 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.591 0.296 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.965 4.834
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 186.6
46: (ns/day) (hour/ns)
46: Performance: 205.387 0.117
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (444 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.570 0.285 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.154 4.657
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 187.0
46: (ns/day) (hour/ns)
46: Performance: 203.757 0.118
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (433 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.614 0.307 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.779 5.022
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 186.9
46: (ns/day) (hour/ns)
46: Performance: 205.895 0.117
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (456 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.570 0.285 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.153 4.658
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 186.8
46: (ns/day) (hour/ns)
46: Performance: 204.176 0.118
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (433 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.551 0.276 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.326 4.506
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 185.8
46: (ns/day) (hour/ns)
46: Performance: 200.730 0.120
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (509 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.665 0.333 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.411 5.441
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 187.0
46: (ns/day) (hour/ns)
46: Performance: 198.979 0.121
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (566 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.622 0.312 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.713 5.093
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 186.0
46: (ns/day) (hour/ns)
46: Performance: 200.592 0.120
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (544 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 1.778 0.889 199.9
46: (ns/day) (hour/ns)
46: Performance: 1.651 14.533
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 186.7
46: (ns/day) (hour/ns)
46: Performance: 201.373 0.119
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (1123 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.867 0.434 199.8
46: (ns/day) (hour/ns)
46: Performance: 3.384 7.092
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 187.0
46: (ns/day) (hour/ns)
46: Performance: 200.149 0.120
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (667 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.554 0.278 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.292 4.535
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 187.0
46: (ns/day) (hour/ns)
46: Performance: 199.585 0.120
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (513 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 2.061 1.031 199.9
46: (ns/day) (hour/ns)
46: Performance: 1.425 16.847
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 186.9
46: (ns/day) (hour/ns)
46: Performance: 199.340 0.120
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (1265 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 1.423 0.712 199.9
46: (ns/day) (hour/ns)
46: Performance: 2.063 11.633
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 188.1
46: (ns/day) (hour/ns)
46: Performance: 186.549 0.129
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (953 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.588 0.295 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.984 4.815
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.015 0.008 188.2
46: (ns/day) (hour/ns)
46: Performance: 187.025 0.128
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (542 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.506 0.254 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.791 4.145
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 185.3
46: (ns/day) (hour/ns)
46: Performance: 198.026 0.121
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (492 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.603 0.302 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.865 4.933
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.013 0.007 186.3
46: (ns/day) (hour/ns)
46: Performance: 206.468 0.116
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as single precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as single precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (545 ms)
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (17392 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 58 tests from 5 test cases ran. (47555 ms total)
46: [ PASSED ] 58 tests.
46/54 Test #46: MdrunNonIntegratorTests ............. Passed 47.64 sec
test 47
Start 47: MdrunTpiTests
47: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunTpiTests.xml"
47: Test timeout computed to be: 600
47: [==========] Running 2 tests from 1 test case.
47: [----------] Global test environment set-up.
47: [----------] 2 tests from Simple/TpiTest
47: [ RUN ] Simple/TpiTest.ReproducesOutput/0
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (4026 ms)
47: [ RUN ] Simple/TpiTest.ReproducesOutput/1
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47:
47: Non-default thread affinity set, disabling internal thread affinity
47:
47: Using 1 OpenMP thread
47:
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (3782 ms)
47: [----------] 2 tests from Simple/TpiTest (7811 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 2 tests from 1 test case ran. (7811 ms total)
47: [ PASSED ] 2 tests.
47/54 Test #47: MdrunTpiTests ....................... Passed 7.88 sec
test 48
Start 48: MdrunMpiTests
48: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiTests.xml"
48: Test timeout computed to be: 600
48: [==========] Running 22 tests from 7 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from DomainDecompositionSpecialCasesTest
48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -151244759
48: Generated 3 of the 3 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 3 of the 3 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 9.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.003 0.001 274.8
48: (ns/day) (hour/ns)
48: Performance: 71.675 0.335
48: This run will generate roughly 0 Mb of data
48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (85 ms)
48: [----------] 1 test from DomainDecompositionSpecialCasesTest (85 ms total)
48:
48: [----------] 4 tests from MimicTest
48: [ RUN ] MimicTest.OneQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -16778249
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.480 0.650 381.5
48: (ns/day) (hour/ns)
48: Performance: 0.133 180.546
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.OneQuantumMol (2037 ms)
48: [ RUN ] MimicTest.AllQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -38013443
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.540 0.665 382.0
48: (ns/day) (hour/ns)
48: Performance: 0.130 184.713
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.AllQuantumMol (2065 ms)
48: [ RUN ] MimicTest.TwoQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -280579
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.500 0.655 381.7
48: (ns/day) (hour/ns)
48: Performance: 0.132 181.938
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.TwoQuantumMol (1972 ms)
48: [ RUN ] MimicTest.BondCuts
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -27348520
48: Generated 2211 of the 2211 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2211 of the 2211 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
48: Number of degrees of freedom in T-Coupling group rest is 66.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: NVE simulation: will use the initial temperature of 300.368 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
48:
48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.500 0.650 384.6
48: (ns/day) (hour/ns)
48: Performance: 0.133 180.542
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.BondCuts (2081 ms)
48: [----------] 4 tests from MimicTest (8155 ms total)
48:
48: [----------] 1 test from MultiSimTerminationTest
48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from MultiSimTerminationTest (0 ms total)
48:
48: [----------] 3 tests from PmeTest
48: [ RUN ] PmeTest.ReproducesEnergies
48: Setting the LD random seed to -310444321
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 8.440 2.150 392.6
48: (ns/day) (hour/ns)
48: Performance: 0.844 28.437
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 8.284 2.110 392.6
48: (ns/day) (hour/ns)
48: Performance: 0.860 27.907
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 8.466 2.155 392.9
48: (ns/day) (hour/ns)
48: Performance: 0.842 28.502
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (29389 ms)
48: [ RUN ] PmeTest.ScalesTheBox
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -143659009
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.370 0.135 274.8
48: (ns/day) (hour/ns)
48: Performance: 0.641 37.441
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.108 0.108 0.108
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBox (1078 ms)
48: [ RUN ] PmeTest.ScalesTheBoxWithWalls
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 1878589269
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Searching the wall atom type(s)
48: Number of degrees of freedom in T-Coupling group rest is 13.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: NVE simulation: will use the initial temperature of 966.268 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.581 0.185 314.2
48: (ns/day) (hour/ns)
48: Performance: 0.468 51.336
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x128, spacing 0.108 0.108 0.118
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBoxWithWalls (63716 ms)
48: [----------] 3 tests from PmeTest (94184 ms total)
48:
48: [----------] 1 test from ReplicaExchangeTerminationTest
48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
48:
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -4.7991020e+01
48: Maximum force = 1.8629866e+02 on atom 13
48: Norm of force = 8.7722033e+01
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (6357 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 3.02331e+02 on atom 3
48: F-Norm = 1.18024e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -5.5862247e+01
48: Maximum force = 4.2727914e+02 on atom 13
48: Norm of force = 1.8453180e+02
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (7998 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.1937704e+02
48: Maximum force = 9.9988633e+03 on atom 9
48: Norm of force = 4.6166993e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (4395 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48:
48: NOTE 3 [file glycine_vacuo.top, line 12]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41575e+04 on atom 10
48: F-Norm = 1.18451e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.5174442e+02
48: Maximum force = 7.4208892e+03 on atom 9
48: Norm of force = 3.5693002e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (5941 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.5698419e+02
48: Maximum force = 4.5704996e+02 on atom 17
48: Norm of force = 1.8327748e+02
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4816 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48:
48: NOTE 4 [file unknown]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 5 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 1.06801e+03 on atom 28
48: F-Norm = 4.26916e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.6941193e+02
48: Maximum force = 2.1835349e+02 on atom 17
48: Norm of force = 7.9216550e+01
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (7081 ms)
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (36595 ms total)
48:
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents converged to Fmax < 10 in 1 steps
48: Potential Energy = -9.7425699e-01
48: Maximum force = 4.0132303e+00 on atom 3
48: Norm of force = 1.6383944e+00
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1627 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 4.01323e+00 on atom 3
48: F-Norm = 1.63839e+00
48:
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
48: Potential Energy = -9.9064207e-01
48: Maximum force = 2.5781622e+00 on atom 3
48: Norm of force = 1.0525302e+00
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2150 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (23 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.1939685e+02
48: Maximum force = 9.9704248e+03 on atom 9
48: Norm of force = 4.6227568e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (3899 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41672e+04 on atom 10
48: F-Norm = 1.19357e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.5625764e+02
48: Maximum force = 7.5018237e+03 on atom 9
48: Norm of force = 3.6139019e+03
48: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as single precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (5400 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1043 ms)
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (14143 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 22 tests from 7 test cases ran. (153164 ms total)
48: [ PASSED ] 22 tests.
48:
48: YOU HAVE 4 DISABLED TESTS
48:
48/54 Test #48: MdrunMpiTests ....................... Passed 153.24 sec
test 49
Start 49: MdrunMpiCoordinationTestsOneRank
49: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
49: Test timeout computed to be: 960
49: [==========] Running 27 tests from 3 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest
49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.362 0.362 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.055 5.919
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.254 0.254 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.776 4.155
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.231 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.349 3.780
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.242 0.243 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.052 3.966
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.232 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.344 3.783
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.242 0.243 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.045 3.970
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1824 ms)
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1824 ms total)
49:
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.191 0.192 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.669 3.129
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.212 0.212 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.913 3.471
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.219 0.220 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.677 3.594
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.197 0.198 99.7
49: (ns/day) (hour/ns)
49: Performance: 7.430 3.230
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.209 0.209 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.014 3.422
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.244 0.245 99.7
49: (ns/day) (hour/ns)
49: Performance: 5.999 4.001
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1488 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.195 0.196 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.513 3.195
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.215 0.215 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.834 3.512
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.255 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.749 4.174
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.229 0.229 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.413 3.742
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.290 0.290 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.061 4.742
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.233 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.296 3.812
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1655 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.240 0.240 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.114 3.926
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.236 0.236 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.216 3.861
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.232 0.233 99.6
49: (ns/day) (hour/ns)
49: Performance: 6.315 3.801
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.202 0.202 99.7
49: (ns/day) (hour/ns)
49: Performance: 7.261 3.305
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.221 0.222 99.6
49: (ns/day) (hour/ns)
49: Performance: 6.627 3.621
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.242 0.243 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.047 3.969
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1589 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.216 0.216 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.800 3.529
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.201 0.202 99.7
49: (ns/day) (hour/ns)
49: Performance: 7.277 3.298
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.231 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.346 3.782
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.233 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.296 3.812
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.255 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.760 4.167
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.233 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.301 3.809
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1621 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.207 0.207 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.096 3.382
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.322 0.322 99.8
49: (ns/day) (hour/ns)
49: Performance: 4.555 5.269
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.396 0.397 99.8
49: (ns/day) (hour/ns)
49: Performance: 3.701 6.485
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.274 0.274 99.7
49: (ns/day) (hour/ns)
49: Performance: 5.355 4.482
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.195 0.196 99.6
49: (ns/day) (hour/ns)
49: Performance: 7.512 3.195
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.238 0.238 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.160 3.896
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1880 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.374 0.374 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.923 6.118
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.141 1.141 100.0
49: (ns/day) (hour/ns)
49: Performance: 1.287 18.651
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.640 0.641 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.292 10.472
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.598 0.598 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.454 9.779
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.489 0.489 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.004 7.990
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.177 0.178 99.7
49: (ns/day) (hour/ns)
49: Performance: 8.258 2.906
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3643 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.228 0.228 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.435 3.730
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.247 0.247 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.950 4.034
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.232 0.232 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.328 3.792
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.243 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.045 3.970
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.244 0.244 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.009 3.994
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.222 0.222 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.610 3.631
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1621 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.262 0.263 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.592 4.292
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.191 0.191 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.689 3.121
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.220 0.221 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.650 3.609
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.231 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.355 3.776
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.233 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.298 3.811
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.233 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.303 3.808
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1578 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.228 0.229 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.428 3.734
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.224 0.225 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.539 3.670
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.275 0.276 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.322 4.509
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.242 0.243 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.054 3.965
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.211 0.211 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.946 3.455
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.210 0.210 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.986 3.435
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1600 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.228 0.229 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.426 3.735
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.236 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.228 3.854
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.220 0.221 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.652 3.608
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.232 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.337 3.787
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.322 0.322 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.560 5.263
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.433 0.433 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.389 7.081
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1876 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.185 0.185 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.941 3.022
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.203 0.204 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.209 3.329
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.208 0.208 99.7
49: (ns/day) (hour/ns)
49: Performance: 7.053 3.403
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.187 0.187 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.848 3.058
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.299 0.300 99.8
49: (ns/day) (hour/ns)
49: Performance: 4.898 4.900
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.467 0.468 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.140 7.643
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1756 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.227 0.228 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.455 3.718
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.247 0.247 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.945 4.037
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.232 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.336 3.788
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.232 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.341 3.785
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.255 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.752 4.172
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.255 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.758 4.168
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1654 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.218 0.218 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.728 3.567
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.214 0.214 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.866 3.495
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.177 0.177 99.9
49: (ns/day) (hour/ns)
49: Performance: 8.313 2.887
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.222 0.222 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.612 3.630
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.211 0.211 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.969 3.444
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.188 0.189 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.790 3.081
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1433 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.207 0.207 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.101 3.380
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.613 0.613 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.394 10.024
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.676 0.676 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.172 11.050
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.654 0.654 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.245 10.690
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.244 0.244 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.008 3.994
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.266 0.267 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.507 4.358
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (2867 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.240 0.240 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.110 3.928
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.214 0.214 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.868 3.495
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.232 0.232 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.334 3.789
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.243 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.046 3.970
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.200 0.200 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.343 3.268
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.178 0.178 99.9
49: (ns/day) (hour/ns)
49: Performance: 8.264 2.904
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1511 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.184 0.184 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.969 3.012
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.257 0.258 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.700 4.211
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.631 0.632 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.325 10.321
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.376 0.376 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.905 6.146
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.277 0.277 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.294 4.534
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.221 0.222 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.622 3.624
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (2155 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.229 0.229 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.413 3.742
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.236 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.228 3.853
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.232 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.336 3.788
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.209 0.210 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.010 3.423
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.199 0.200 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.351 3.265
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.189 0.189 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.771 3.089
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1500 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.218 0.218 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.736 3.563
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.236 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.235 3.849
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.253 0.254 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.784 4.150
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.609 0.609 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.410 9.957
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.222 0.222 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.613 3.629
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.244 0.244 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.013 3.991
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1989 ms)
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (33419 ms total)
49:
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.220 0.220 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.666 3.600
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.214 0.214 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.858 3.500
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.227 0.227 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.460 3.715
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.237 0.238 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.175 3.887
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.196 0.197 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.471 3.212
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.201 0.202 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.288 3.293
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (21099 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.235 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.240 3.846
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.244 0.244 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.009 3.994
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.246 0.247 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.950 4.033
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.251 0.252 99.7
49: (ns/day) (hour/ns)
49: Performance: 5.835 4.113
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.244 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.027 3.982
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.220 0.220 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.672 3.597
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (22243 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.227 0.228 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.455 3.718
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.248 0.248 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.920 4.054
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.211 0.212 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.941 3.458
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.238 0.238 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.171 3.889
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.234 0.235 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.251 3.839
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.255 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.749 4.175
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (22569 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.239 0.240 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.129 3.916
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.268 0.268 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.481 4.379
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.217 0.218 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.750 3.555
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.235 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.239 3.847
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.243 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.045 3.970
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.256 0.256 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.730 4.188
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (22628 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.212 0.212 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.918 3.469
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.217 0.217 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.762 3.549
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.248 0.248 99.7
49: (ns/day) (hour/ns)
49: Performance: 5.919 4.055
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.259 0.259 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.662 4.239
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.233 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.294 3.813
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.198 0.199 99.7
49: (ns/day) (hour/ns)
49: Performance: 7.399 3.244
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (22710 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.217 0.217 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.766 3.547
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.238 0.238 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.162 3.895
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.238 0.239 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.154 3.900
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.211 0.212 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.937 3.460
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.216 0.217 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.769 3.546
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.271 0.272 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.409 4.437
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (22505 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.266 0.266 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.524 4.345
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.467 0.467 100.0
49: (ns/day) (hour/ns)
49: Performance: 3.145 7.632
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.221 0.221 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.650 3.609
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.208 0.208 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.049 3.405
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.286 0.286 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.138 4.671
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.227 0.227 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.468 3.710
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (22859 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.232 0.232 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.334 3.789
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.302 0.302 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.863 4.935
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.235 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.257 3.836
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.292 0.292 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.031 4.771
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.249 0.249 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.894 4.072
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.215 0.216 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.815 3.522
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (22765 ms)
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (179379 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 27 tests from 3 test cases ran. (214623 ms total)
49: [ PASSED ] 27 tests.
49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 214.71 sec
test 50
Start 50: MdrunMpiCoordinationTestsTwoRanks
50: Test command: /<<PKGBUILDDIR>>/build/basic/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
50: Test timeout computed to be: 960
50: [==========] Running 27 tests from 3 test cases.
50: [----------] Global test environment set-up.
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest
50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.449 0.225 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.527 3.677
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.429 0.215 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.822 3.518
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.397 0.199 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.379 3.253
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.465 0.233 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.301 3.809
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.447 0.224 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.552 3.663
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.456 0.229 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.423 3.737
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1662 ms)
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1663 ms total)
50:
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.459 0.230 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.394 3.754
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.485 0.243 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.041 3.973
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.458 0.230 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.399 3.750
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.437 0.219 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.714 3.575
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.462 0.232 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.339 3.786
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.445 0.225 197.9
50: (ns/day) (hour/ns)
50: Performance: 6.533 3.673
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1595 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.379 0.190 199.6
50: (ns/day) (hour/ns)
50: Performance: 7.745 3.099
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.397 0.199 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.368 3.257
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.391 0.196 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.495 3.202
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.435 0.218 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.728 3.567
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.461 0.231 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.357 3.775
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.461 0.231 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.359 3.774
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1483 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.434 0.218 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.750 3.556
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.464 0.233 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.313 3.802
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.480 0.241 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.099 3.935
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.458 0.230 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.399 3.751
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.444 0.223 199.1
50: (ns/day) (hour/ns)
50: Performance: 6.591 3.642
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.384 0.193 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.615 3.152
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1555 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.389 0.195 199.7
50: (ns/day) (hour/ns)
50: Performance: 7.535 3.185
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.397 0.199 199.6
50: (ns/day) (hour/ns)
50: Performance: 7.380 3.252
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.412 0.207 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.097 3.381
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.479 0.240 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.116 3.924
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.501 0.251 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.841 4.109
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.438 0.220 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.685 3.590
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1533 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.455 0.228 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.440 3.727
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.478 0.239 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.138 3.910
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.441 0.221 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.637 3.616
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.460 0.231 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.364 3.771
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.167 0.584 199.7
50: (ns/day) (hour/ns)
50: Performance: 2.514 9.548
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.500 0.751 199.8
50: (ns/day) (hour/ns)
50: Performance: 1.956 12.269
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (2501 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.387 0.694 199.9
50: (ns/day) (hour/ns)
50: Performance: 2.116 11.340
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.157 0.579 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.536 9.462
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.197 0.600 199.6
50: (ns/day) (hour/ns)
50: Performance: 2.448 9.802
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.419 0.211 199.0
50: (ns/day) (hour/ns)
50: Performance: 6.977 3.440
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.682 0.342 199.5
50: (ns/day) (hour/ns)
50: Performance: 4.294 5.589
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.473 0.238 198.8
50: (ns/day) (hour/ns)
50: Performance: 6.167 3.892
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2950 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.438 0.219 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.694 3.585
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.449 0.225 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.522 3.680
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.434 0.218 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.749 3.556
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.582 0.292 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.033 4.768
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.365 0.183 199.2
50: (ns/day) (hour/ns)
50: Performance: 8.025 2.991
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.391 0.196 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.481 3.208
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (1614 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.389 0.195 199.6
50: (ns/day) (hour/ns)
50: Performance: 7.542 3.182
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.396 0.199 199.5
50: (ns/day) (hour/ns)
50: Performance: 7.394 3.246
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.396 0.199 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.398 3.244
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.421 0.211 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.956 3.450
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.466 0.233 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.291 3.815
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.466 0.234 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.288 3.817
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1535 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.485 0.243 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.049 3.968
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.430 0.215 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.816 3.521
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.417 0.209 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.024 3.417
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.407 0.205 199.1
50: (ns/day) (hour/ns)
50: Performance: 7.180 3.342
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.405 0.204 199.0
50: (ns/day) (hour/ns)
50: Performance: 7.217 3.325
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.365 0.183 198.9
50: (ns/day) (hour/ns)
50: Performance: 8.011 2.996
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1542 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.430 0.216 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.814 3.522
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.387 0.194 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.568 3.171
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.449 0.225 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.515 3.684
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.473 0.237 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.192 3.876
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.410 0.206 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.134 3.364
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.495 0.248 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.916 4.057
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1568 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.485 0.243 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.044 3.971
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.535 0.268 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.478 4.381
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.483 0.242 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.060 3.960
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.531 0.266 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.519 4.348
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.392 0.197 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.465 3.215
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.416 0.209 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.043 3.408
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1697 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.365 0.183 199.6
50: (ns/day) (hour/ns)
50: Performance: 8.035 2.987
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.483 0.242 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.059 3.961
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.453 0.228 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.456 3.717
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.454 0.230 197.0
50: (ns/day) (hour/ns)
50: Performance: 6.376 3.764
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.445 0.223 199.1
50: (ns/day) (hour/ns)
50: Performance: 6.575 3.650
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.455 0.229 199.1
50: (ns/day) (hour/ns)
50: Performance: 6.427 3.734
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1589 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.455 0.228 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.441 3.726
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.195 0.599 199.7
50: (ns/day) (hour/ns)
50: Performance: 2.454 9.781
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.670 0.836 199.8
50: (ns/day) (hour/ns)
50: Performance: 1.758 13.653
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.369 0.686 199.6
50: (ns/day) (hour/ns)
50: Performance: 2.142 11.205
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.457 0.230 199.0
50: (ns/day) (hour/ns)
50: Performance: 6.399 3.750
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.390 0.196 198.7
50: (ns/day) (hour/ns)
50: Performance: 7.485 3.206
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (3000 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.468 0.235 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.263 3.832
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.721 0.361 199.7
50: (ns/day) (hour/ns)
50: Performance: 4.066 5.903
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.847 0.424 199.6
50: (ns/day) (hour/ns)
50: Performance: 3.460 6.936
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.268 0.635 199.7
50: (ns/day) (hour/ns)
50: Performance: 2.313 10.376
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.483 0.242 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.059 3.961
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.477 0.239 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.140 3.909
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (2399 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.367 0.184 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.976 3.009
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.405 0.704 199.5
50: (ns/day) (hour/ns)
50: Performance: 2.086 11.507
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.438 0.220 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.674 3.596
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.435 0.218 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.725 3.569
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.416 0.209 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.035 3.412
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.482 0.242 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.066 3.956
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (2000 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.453 0.227 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.472 3.708
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.409 0.205 199.5
50: (ns/day) (hour/ns)
50: Performance: 7.164 3.350
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.390 0.196 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.510 3.196
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.411 0.206 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.114 3.374
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.526 0.264 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.567 4.311
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.460 0.231 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.363 3.772
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1580 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.423 0.212 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.941 3.458
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.458 0.230 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.396 3.752
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.479 0.240 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.118 3.923
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.476 0.239 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.154 3.900
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.461 0.231 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.358 3.775
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.459 0.230 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.379 3.762
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1620 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.387 0.194 199.6
50: (ns/day) (hour/ns)
50: Performance: 7.567 3.172
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.372 0.186 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.880 3.046
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.411 0.206 199.1
50: (ns/day) (hour/ns)
50: Performance: 7.122 3.370
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.454 0.228 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.442 3.726
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.497 0.249 199.3
50: (ns/day) (hour/ns)
50: Performance: 5.890 4.075
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.460 0.231 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.364 3.771
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as single precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1534 ms)
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (33300 ms total)
50:
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.509 0.255 199.7
50: (ns/day) (hour/ns)
50: Performance: 5.768 4.161
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.459 0.230 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.383 3.760
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.445 0.223 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.582 3.646
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.604 0.315 191.8
50: (ns/day) (hour/ns)
50: Performance: 4.664 5.146
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.468 0.235 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.259 3.835
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.565 0.283 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.184 4.630
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (22439 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.430 0.215 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.822 3.518
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.423 0.214 197.2
50: (ns/day) (hour/ns)
50: Performance: 6.850 3.503
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.425 0.214 199.1
50: (ns/day) (hour/ns)
50: Performance: 6.875 3.491
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.455 0.228 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.436 3.729
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.433 0.217 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.762 3.549
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.463 0.232 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.322 3.797
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (22324 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.486 0.244 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.030 3.980
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.483 0.242 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.062 3.959
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.489 0.245 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.990 4.007
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.468 0.235 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.261 3.833
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.477 0.239 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.139 3.909
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.503 0.252 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.821 4.123
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (21399 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.435 0.218 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.740 3.561
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.517 0.259 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.664 4.237
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.392 0.197 199.0
50: (ns/day) (hour/ns)
50: Performance: 7.449 3.222
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.446 0.224 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.560 3.659
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.459 0.230 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.382 3.761
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.474 0.238 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.176 3.886
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (21598 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.489 0.245 199.7
50: (ns/day) (hour/ns)
50: Performance: 5.992 4.005
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.462 0.232 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.342 3.785
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.473 0.239 198.1
50: (ns/day) (hour/ns)
50: Performance: 6.155 3.899
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.444 0.223 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.586 3.644
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.445 0.223 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.589 3.643
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.400 0.201 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.319 3.279
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (22259 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.487 0.244 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.022 3.985
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.523 0.262 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.608 4.280
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.492 0.247 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.949 4.034
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.502 0.252 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.836 4.112
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.499 0.250 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.871 4.088
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.463 0.232 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.321 3.797
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (23205 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.481 0.242 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.082 3.946
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.472 0.237 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.206 3.868
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.565 0.284 199.1
50: (ns/day) (hour/ns)
50: Performance: 5.174 4.639
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.520 0.261 199.0
50: (ns/day) (hour/ns)
50: Performance: 5.620 4.270
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.467 0.235 198.9
50: (ns/day) (hour/ns)
50: Performance: 6.254 3.838
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.500 0.252 198.9
50: (ns/day) (hour/ns)
50: Performance: 5.840 4.110
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (22653 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.474 0.238 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.181 3.883
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.452 0.228 198.6
50: (ns/day) (hour/ns)
50: Performance: 6.455 3.718
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.522 0.263 198.4
50: (ns/day) (hour/ns)
50: Performance: 5.581 4.300
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.437 0.220 198.9
50: (ns/day) (hour/ns)
50: Performance: 6.687 3.589
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.516 0.259 199.0
50: (ns/day) (hour/ns)
50: Performance: 5.669 4.234
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.502 0.252 199.1
50: (ns/day) (hour/ns)
50: Performance: 5.827 4.118
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as single precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as single precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (22098 ms)
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (177979 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 27 tests from 3 test cases ran. (212943 ms total)
50: [ PASSED ] 27 tests.
50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 213.03 sec
test 51
Start 51: GmxapiExternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 9 tests from 2 test cases.
51: [----------] Global test environment set-up.
51: [----------] 8 tests from GmxApiTest
51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
51: Setting the LD random seed to 833613775
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.523 0.262 199.8
51: (ns/day) (hour/ns)
51: Performance: 1.933 12.417
51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (3769 ms)
51: [ RUN ] GmxApiTest.SystemConstruction
51: Setting the LD random seed to -134340618
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.SystemConstruction (3565 ms)
51: [ RUN ] GmxApiTest.SaneVersionComparisons
51: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
51: [ RUN ] GmxApiTest.VersionNamed0_1_Features
51: [ OK ] GmxApiTest.VersionNamed0_1_Features (1 ms)
51: [ RUN ] GmxApiTest.RunnerBasicMD
51: Setting the LD random seed to -121898098
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.577 0.289 199.8
51: (ns/day) (hour/ns)
51: Performance: 1.753 13.690
51: [ OK ] GmxApiTest.RunnerBasicMD (3881 ms)
51: [ RUN ] GmxApiTest.RunnerReinitialize
51: Setting the LD random seed to 2071813501
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51:
51: Received the remote INT/TERM signal, stopping within 50 steps
51:
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.585 0.293 199.7
51: (ns/day) (hour/ns)
51: Performance: 12.104 1.983
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.572 0.287 199.3
51: (ns/day) (hour/ns)
51: Performance: 12.357 1.942
51: [ OK ] GmxApiTest.RunnerReinitialize (3915 ms)
51: [ RUN ] GmxApiTest.RunnerContinuedMD
51: Setting the LD random seed to -35940387
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 10 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.486 0.243 199.7
51: (ns/day) (hour/ns)
51: Performance: 7.626 3.147
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.545 0.273 199.5
51: (ns/day) (hour/ns)
51: Performance: 12.980 1.849
51: [ OK ] GmxApiTest.RunnerContinuedMD (3906 ms)
51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
51: Setting the LD random seed to -1211115489
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 1 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.511 0.256 199.8
51: (ns/day) (hour/ns)
51: Performance: 1.318 18.206
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51:
51: Using 1 MPI thread
51:
51: Non-default thread affinity set, disabling internal thread affinity
51:
51: Using 2 OpenMP threads
51:
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.614 0.308 199.7
51: (ns/day) (hour/ns)
51: Performance: 1.097 21.874
51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (3861 ms)
51: [----------] 8 tests from GmxApiTest (22901 ms total)
51:
51: [----------] 1 test from GmxApiBasicTest
51: [ RUN ] GmxApiBasicTest.Status
51: [ OK ] GmxApiBasicTest.Status (0 ms)
51: [----------] 1 test from GmxApiBasicTest (0 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 9 tests from 2 test cases ran. (22903 ms total)
51: [ PASSED ] 9 tests.
51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 23.00 sec
test 52
Start 52: GmxapiMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 9 tests from 2 test cases.
52: [----------] Global test environment set-up.
52: [----------] 8 tests from GmxApiTest
52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
52: Setting the LD random seed to -1073749549
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.534 0.268 199.8
52: (ns/day) (hour/ns)
52: Performance: 1.892 12.683
52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (3754 ms)
52: [ RUN ] GmxApiTest.SystemConstruction
52: Setting the LD random seed to -25200145
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.SystemConstruction (3581 ms)
52: [ RUN ] GmxApiTest.SaneVersionComparisons
52: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
52: [ RUN ] GmxApiTest.VersionNamed0_1_Features
52: [ OK ] GmxApiTest.VersionNamed0_1_Features (1 ms)
52: [ RUN ] GmxApiTest.RunnerBasicMD
52: Setting the LD random seed to 2144837573
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.537 0.269 199.8
52: (ns/day) (hour/ns)
52: Performance: 1.882 12.752
52: [ OK ] GmxApiTest.RunnerBasicMD (3817 ms)
52: [ RUN ] GmxApiTest.RunnerReinitialize
52: Setting the LD random seed to 1597765046
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52:
52: Received the remote INT/TERM signal, stopping within 50 steps
52:
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.574 0.288 199.7
52: (ns/day) (hour/ns)
52: Performance: 12.322 1.948
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.530 0.265 199.6
52: (ns/day) (hour/ns)
52: Performance: 13.352 1.797
52: [ OK ] GmxApiTest.RunnerReinitialize (4034 ms)
52: [ RUN ] GmxApiTest.RunnerContinuedMD
52: Setting the LD random seed to -2113542
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 10 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.548 0.275 199.7
52: (ns/day) (hour/ns)
52: Performance: 6.762 3.549
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.526 0.264 199.5
52: (ns/day) (hour/ns)
52: Performance: 13.442 1.785
52: [ OK ] GmxApiTest.RunnerContinuedMD (4055 ms)
52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
52: Setting the LD random seed to 2092818359
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 1 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.936 0.468 199.9
52: (ns/day) (hour/ns)
52: Performance: 0.721 33.286
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Raspbian-2020.6-2 (single precision)
52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52:
52: Using 1 MPI thread
52: Using 2 OpenMP threads
52:
52:
52: NOTE: The number of threads is not equal to the number of (logical) cores
52: and the -pin option is set to auto: will not pin threads to cores.
52: This can lead to significant performance degradation.
52: Consider using -pin on (and -pinoffset in case you run multiple jobs).
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.475 0.238 199.7
52: (ns/day) (hour/ns)
52: Performance: 1.418 16.925
52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4221 ms)
52: [----------] 8 tests from GmxApiTest (23463 ms total)
52:
52: [----------] 1 test from GmxApiBasicTest
52: [ RUN ] GmxApiBasicTest.Status
52: [ OK ] GmxApiBasicTest.Status (0 ms)
52: [----------] 1 test from GmxApiBasicTest (1 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 9 tests from 2 test cases ran. (23464 ms total)
52: [ PASSED ] 9 tests.
52/54 Test #52: GmxapiMpiTests ...................... Passed 23.56 sec
test 53
Start 53: GmxapiInternalInterfaceTests
53: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 2 tests from 1 test case.
53: [----------] Global test environment set-up.
53: [----------] 2 tests from GmxApiTest
53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
53: Setting the LD random seed to 2136616431
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (3412 ms)
53: [ RUN ] GmxApiTest.CreateApiWorkflow
53: Setting the LD random seed to -1241546829
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.CreateApiWorkflow (3491 ms)
53: [----------] 2 tests from GmxApiTest (6903 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 2 tests from 1 test case ran. (6904 ms total)
53: [ PASSED ] 2 tests.
53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 6.98 sec
test 54
Start 54: GmxapiInternalsMpiTests
54: Test command: /<<PKGBUILDDIR>>/build/basic/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic/Testing/Temporary/GmxapiInternalsMpiTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 2 tests from 1 test case.
54: [----------] Global test environment set-up.
54: [----------] 2 tests from GmxApiTest
54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
54: Setting the LD random seed to -202653841
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (3216 ms)
54: [ RUN ] GmxApiTest.CreateApiWorkflow
54: Setting the LD random seed to 805298618
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.CreateApiWorkflow (3188 ms)
54: [----------] 2 tests from GmxApiTest (6404 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 2 tests from 1 test case ran. (6405 ms total)
54: [ PASSED ] 2 tests.
54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 6.48 sec
100% tests passed, 0 tests failed out of 54
Label Time Summary:
GTest = 891.82 sec*proc (54 tests)
IntegrationTest = 384.19 sec*proc (12 tests)
MpiTest = 611.47 sec*proc (8 tests)
SlowTest = 427.73 sec*proc (2 tests)
UnitTest = 79.90 sec*proc (40 tests)
Total Test time (real) = 892.45 sec
/usr/bin/make -j4 -C build/basic-dp tests
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/make -f CMakeFiles/Makefile2 tests
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/basic-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 96
/usr/bin/make -f CMakeFiles/Makefile2 CMakeFiles/tests.dir/all
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Raspbian-2020.6-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/basic-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.6-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/selection/CMakeFiles/scanner.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/tng_io_obj.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
[ 0%] Built target scanner
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
[ 1%] Built target tng_io_obj
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/thread_mpi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
[ 1%] Built target release-version-info
[ 3%] Built target thread_mpi
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/CMakeFiles/vmddlopen.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/lmfit_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 4%] Built target lmfit_objlib
/usr/bin/make -f src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build.make src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/fileio/CMakeFiles/vmddlopen.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googletest /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/DependInfo.cmake --color=
[ 4%] Built target linearalgebra
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
[ 4%] Built target vmddlopen
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs /<<PKGBUILDDIR>>/build/basic-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target gtest
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build.make src/external/googletest/googlemock/gtest/CMakeFiles/gtest.dir/build
[ 5%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CREATE_SHARED_LIBRARY=1 -Dgtest_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googletest/include -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -std=c++14 -o CMakeFiles/gtest.dir/src/gtest-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googletest/src/gtest-all.cc
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/programs/CMakeFiles/mdrun_objlib.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 5%] Built target mdrun_objlib
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/gromacs/CMakeFiles/libgromacs.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 65%] Built target libgromacs
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/CMakeFiles/gmxapi.dir/DependInfo.cmake --color=
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/CMakeFiles/gmxapi.dir/build.make src/api/cpp/CMakeFiles/gmxapi.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'src/api/cpp/CMakeFiles/gmxapi.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 66%] Built target gmxapi
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/gtest && /usr/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgtest.so -o ../../../../../lib/libgtest.so CMakeFiles/gtest.dir/src/gtest-all.cc.o -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 66%] Built target gtest
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock/CMakeFiles/gmock.dir/DependInfo.cmake --color=
Scanning dependencies of target gmock
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/external/googletest/googlemock/CMakeFiles/gmock.dir/build.make src/external/googletest/googlemock/CMakeFiles/gmock.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/c++ -DGMX_DOUBLE=1 -DGTEST_CAN_STREAM_RESULTS=0 -DGTEST_CREATE_SHARED_LIBRARY=1 -D_GNU_SOURCE=1 -Dgmock_EXPORTS -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -I/<<PKGBUILDDIR>>/src/external/googletest/googlemock -I/<<PKGBUILDDIR>>/src/external/googletest/googletest -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wshadow -DGTEST_HAS_PTHREAD=1 -fexceptions -Wextra -Wno-unused-parameter -Wno-missing-field-initializers -Wno-deprecated-copy -std=c++14 -o CMakeFiles/gmock.dir/src/gmock-all.cc.o -c /<<PKGBUILDDIR>>/src/external/googletest/googlemock/src/gmock-all.cc
cd /<<PKGBUILDDIR>>/build/basic-dp/src/external/googletest/googlemock && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmock.dir/link.txt --verbose=1
/usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now -shared -Wl,-soname,libgmock.so -o ../../../../lib/libgmock.so CMakeFiles/gmock.dir/src/gmock-all.cc.o -lpthread ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 66%] Built target gmock
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/CMakeFiles/testutils.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/CMakeFiles/testutils.dir/build.make src/testutils/CMakeFiles/testutils.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/cmdlinetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/cmdlinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/conftest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/conftest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/filematchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/filematchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/interactivetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/loggertest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/loggertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpi_printer.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpi_printer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/mpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/refdata_xml.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/refdata_xml.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/simulationdatabase.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/simulationdatabase.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stdiohelper.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stdiohelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/stringtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/stringtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testasserts.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testasserts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfilemanager.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfilemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testfileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testfileredirector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testinit.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testinit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/testoptions.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/testoptions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/textblockmatchers.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/textblockmatchers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tprfilegenerator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/xvgtest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/xvgtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o -c /<<PKGBUILDDIR>>/src/external/tinyxml2/tinyxml2.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/cmake -P CMakeFiles/testutils.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libtestutils.a CMakeFiles/testutils.dir/cmdlinetest.cpp.o CMakeFiles/testutils.dir/conftest.cpp.o CMakeFiles/testutils.dir/filematchers.cpp.o CMakeFiles/testutils.dir/interactivetest.cpp.o CMakeFiles/testutils.dir/loggertest.cpp.o CMakeFiles/testutils.dir/mpi_printer.cpp.o CMakeFiles/testutils.dir/mpitest.cpp.o CMakeFiles/testutils.dir/refdata.cpp.o CMakeFiles/testutils.dir/refdata_xml.cpp.o CMakeFiles/testutils.dir/simulationdatabase.cpp.o CMakeFiles/testutils.dir/stdiohelper.cpp.o CMakeFiles/testutils.dir/stringtest.cpp.o CMakeFiles/testutils.dir/testasserts.cpp.o CMakeFiles/testutils.dir/testfilemanager.cpp.o CMakeFiles/testutils.dir/testfileredirector.cpp.o CMakeFiles/testutils.dir/testinit.cpp.o CMakeFiles/testutils.dir/testmatchers.cpp.o CMakeFiles/testutils.dir/testoptions.cpp.o CMakeFiles/testutils.dir/textblockmatchers.cpp.o CMakeFiles/testutils.dir/tprfilegenerator.cpp.o CMakeFiles/testutils.dir/xvgtest.cpp.o CMakeFiles/testutils.dir/__/external/tinyxml2/tinyxml2.cpp.o
/usr/bin/ranlib ../../lib/libtestutils.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/depend
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/depend
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/CMakeFiles/testutils-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/DependInfo.cmake --color=
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/DependInfo.cmake --color=
Scanning dependencies of target testutils-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/mpitest.cpp
Scanning dependencies of target utility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-mpi-test.dir/build
Scanning dependencies of target testutils-test
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator_mpi.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/testutils/tests/CMakeFiles/testutils-test.dir/build.make src/testutils/tests/CMakeFiles/testutils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/interactivetest.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/interactivetest.cpp
Scanning dependencies of target mdrun_test_infrastructure
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun_test_infrastructure.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energyreader.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-mpi-test.dir/mpitest.cpp.o CMakeFiles/testutils-mpi-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-mpi-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/energycomparison.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-mpi-test.dir/physicalnodecommunicator_mpi.cpp.o CMakeFiles/utility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target testutils-mpi-test
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/CMakeFiles/utility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target utility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build.make src/gromacs/utility/tests/CMakeFiles/utility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/alignedallocator.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 68%] Built target utility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/refdata_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/arrayref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/arrayref.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mdmodulenotification.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/testasserts_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/terminationhelper.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectorycomparison.cpp
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdlib-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build.make src/gromacs/mdlib/tests/CMakeFiles/mdlib-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/tests/xvgtest_tests.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/testutils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/testutils/../external/tinyxml2 -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/testutils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/testutils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/testutils-test.dir/interactivetest.cpp.o CMakeFiles/testutils-test.dir/refdata_tests.cpp.o CMakeFiles/testutils-test.dir/testasserts_tests.cpp.o CMakeFiles/testutils-test.dir/xvgtest_tests.cpp.o CMakeFiles/testutils-test.dir/__/unittest_main.cpp.o -o ../../../bin/testutils-test ../../../lib/libtestutils.a ../../../lib/libgromacs_d.so.5.0.0 ../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../lib/libgtest.so -lpthread
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/stl_vector.h: In function 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 69%] Built target testutils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask32.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask32.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectoryreader.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_SingleConstraint_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:331:51: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
331 | std::vector<real> masses = { 1.0, 12.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:333:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
333 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TwoDisjointConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:377:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
377 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:379:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
379 | std::vector<real> constraintsR0 = { 2.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:384:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
384 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:388:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
388 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:390:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
390 | std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:431:50: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
431 | std::vector<real> constraintsR0 = { 0.1, 0.2 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:438:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
438 | { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:440:101: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
440 | std::vector<RVec> xPrime = { { 0.08, 0.07, 0.01 }, { -0.02, 0.01, -0.02 }, { 0.10, 0.12, 0.11 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:442:85: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
442 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }, { 0.0, 0.0, 1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_ThreeConstraintsWithCentralAtom_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:481:61: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
481 | std::vector<real> masses = { 12.0, 1.0, 1.0, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:483:45: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
483 | std::vector<real> constraintsR0 = { 0.1 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:488:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
488 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:493:59: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
493 | { -0.005, 0.011, 0.102 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:495:104: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
495 | std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_FourSequentialConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:534:67: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
534 | std::vector<real> masses = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:541:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
541 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:545:5: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
545 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:547:106: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
547 | std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp: In member function 'virtual void gmx::test::{anonymous}::ConstraintsTest_TriangleOfConstraints_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:594:63: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
594 | { 0.0, 0.0, oneTenthOverSqrtTwo } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:596:103: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
596 | std::vector<RVec> xPrime = { { 0.09, -0.02, 0.01 }, { -0.02, 0.10, -0.02 }, { 0.03, -0.01, 0.07 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constr.cpp:598:88: note: parameter passing for argument of type 'std::initializer_list<gmx::BasicVector<double> >' changed in GCC 7.1
598 | std::vector<RVec> v = { { 1.0, 1.0, 1.0 }, { -2.0, -2.0, -2.0 }, { 1.0, 1.0, 1.0 } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -P CMakeFiles/mdrun_test_infrastructure.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun_test_infrastructure.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrun_test_infrastructure.a CMakeFiles/mdrun_test_infrastructure.dir/energyreader.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/energycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/moduletest.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/mdmodulenotification.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/terminationhelper.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectorycomparison.cpp.o CMakeFiles/mdrun_test_infrastructure.dir/trajectoryreader.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrun_test_infrastructure.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target mdrun_test_infrastructure
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/DependInfo.cmake --color=
Scanning dependencies of target applied_forces-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build.make src/gromacs/applied_forces/tests/CMakeFiles/applied_forces-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfitting.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/mock_helptopic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingoptions.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestdata.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::ConstraintsTestData::ConstraintsTestData(const string&, int, std::vector<double>, std::vector<int>, std::vector<double>, bool, real (*)[3], bool, float, real, real, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, const std::vector<gmx::BasicVector<double> >&, real, gmx_bool, int, int, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -P CMakeFiles/onlinehelp-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libonlinehelp-test-shared.a CMakeFiles/onlinehelp-test-shared.dir/mock_helptopic.cpp.o
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/constrtestrunners.cpp
/usr/bin/ranlib ../../../../lib/libonlinehelp-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target onlinehelp-test-shared
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/DependInfo.cmake --color=
Scanning dependencies of target domdec-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build.make src/gromacs/domdec/tests/CMakeFiles/domdec-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/hashedmap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/hashedmap.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/ebin.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/tests/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/domdec/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/domdec/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/domdec-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/domdec-test.dir/hashedmap.cpp.o CMakeFiles/domdec-test.dir/localatomsetmanager.cpp.o CMakeFiles/domdec-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/domdec-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 70%] Built target domdec-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/expanded.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/tests/electricfield.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::{anonymous}::ElectricFieldTest::test(int, real, real, real, real, real)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/applied_forces/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/DependInfo.cmake --color=
Scanning dependencies of target ewald-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build.make src/gromacs/ewald/tests/CMakeFiles/ewald-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmebsplinetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/applied_forces/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/applied_forces-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/applied_forces-test.dir/densityfitting.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingoptions.cpp.o CMakeFiles/applied_forces-test.dir/densityfittingamplitudelookup.cpp.o CMakeFiles/applied_forces-test.dir/electricfield.cpp.o CMakeFiles/applied_forces-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/applied_forces-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target applied_forces-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrog.cpp
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/CMakeFiles/fft-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fft-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build.make src/gromacs/fft/tests/CMakeFiles/fft-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/tests/fft.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fft/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fft/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fft-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fft-test.dir/fft.cpp.o CMakeFiles/fft-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fft-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 71%] Built target fft-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_grp_tcstat&}; _Tp = t_grp_tcstat; _Alloc = std::allocator<t_grp_tcstat>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_grp_tcstat>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::LeapFrogTestData::LeapFrogTestData(int, real, const real*, const real*, int, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.cpp:43:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_grp_tcstat*, std::vector<t_grp_tcstat> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestdata.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/leapfrogtestrunners.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::integrateLeapFrogSimple(gmx::test::LeapFrogTestData*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesolvetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settle.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static void gmx::test::{anonymous}::PmeGatherTest::SetUpTestCase()':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:79:80: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
79 | 2.86F, 0.24F, 5.76F, 5.19F, 0.72F };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:118:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
118 | };
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmegathertest.cpp:146:1: note: parameter passing for argument of type 'std::initializer_list<double>' changed in GCC 7.1
146 | };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask64.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask64.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestrunners.cpp
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gpu_utils-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build.make src/gromacs/gpu_utils/tests/CMakeFiles/gpu_utils-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/gputest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/gputest.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/bitmask128.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/bitmask128.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/settletestdata.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::test::SettleTestData::SettleTestData(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/block.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/shake.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<double> gmx::{anonymous}::computeDisplacements(const std::vector<int>&, const std::vector<double>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest::SetUp()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::{anonymous}::ShakeTest::runTest(size_t, size_t, const std::vector<int>&, const std::vector<double>&, const std::vector<double>&, const std::vector<double>&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-port.h:279,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/internal/gtest-linked_ptr.h:74,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-port.h:53,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-generated-internal-utils.h:44,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/internal/gmock-internal-utils.h:45,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock-actions.h:46,
from /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include/gmock/gmock.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(_InputIterator, _InputIterator, const allocator_type&) [with _InputIterator = __gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >; <template-parameter-2-2> = void; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
653 | vector(_InputIterator __first, _InputIterator __last,
| ^~~~~~
/usr/include/c++/10/bits/stl_vector.h:653:2: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsThreeBondsWithCommonAtoms_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoBondsWithACommonAtom_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsTwoDisjointBonds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ShakeTest_ConstrainsOneBond_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/simulationsignal.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:325:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
325 | c_sampleCoordinatesFull.begin() + 1);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:328:81: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
328 | c_sampleCoordinatesFull.begin() + 3);
| ^
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmesplinespreadtest.cpp:331:83: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<const gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
331 | c_sampleCoordinatesFull.begin() + 16);
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/defaultinitializationallocator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/enumerationhelpers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroups.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_butaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethaneUA_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_methane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_ethane_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterThreeSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp: In function 'void gmx::test::pmeInitAtoms(gmx_pme_t*, gmx::StatePropagatorDataGpu*, gmx::test::CodePath, const CoordinatesVector&, const ChargesVector&)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/tests/pmetestcommon.cpp:201:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
201 | stateGpu->copyCoordinatesToGpu(arrayRefFromArray(coordinates.data(), coordinates.size()),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
202 | gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFourSite_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_waterFlexAngle_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroups_twoMoltypes_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/fixedcapacityvector.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/tests/testhardwarecontexts.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_iparams&}; _Tp = t_iparams; _Alloc = std::allocator<t_iparams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_iparams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/inmemoryserializer.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::{anonymous}::UpdateGroupsCog_ComputesCogs_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_iparams*, std::vector<t_iparams> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
137 | updateGroupsCog.addCogs(globalAtomIndices, positions);
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/tests/updategroupscog.cpp:137:28: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/ewald/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests/Testing/Temporary\" -DTEST_USES_HARDWARE_DETECTION=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdlib/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/ewald/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ewald-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/ewald-test.dir/pmebsplinetest.cpp.o CMakeFiles/ewald-test.dir/pmegathertest.cpp.o CMakeFiles/ewald-test.dir/pmesolvetest.cpp.o CMakeFiles/ewald-test.dir/pmesplinespreadtest.cpp.o CMakeFiles/ewald-test.dir/pmetestcommon.cpp.o CMakeFiles/ewald-test.dir/testhardwarecontexts.cpp.o CMakeFiles/ewald-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/ewald-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 72%] Built target ewald-test
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/DependInfo.cmake --color=
Scanning dependencies of target hardware-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build.make src/gromacs/hardware/tests/CMakeFiles/hardware-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/tests/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdlib-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdlib-test.dir/calc_verletbuf.cpp.o CMakeFiles/mdlib-test.dir/constr.cpp.o CMakeFiles/mdlib-test.dir/constrtestdata.cpp.o CMakeFiles/mdlib-test.dir/constrtestrunners.cpp.o CMakeFiles/mdlib-test.dir/ebin.cpp.o CMakeFiles/mdlib-test.dir/energyoutput.cpp.o CMakeFiles/mdlib-test.dir/expanded.cpp.o CMakeFiles/mdlib-test.dir/leapfrog.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestdata.cpp.o CMakeFiles/mdlib-test.dir/leapfrogtestrunners.cpp.o CMakeFiles/mdlib-test.dir/settle.cpp.o CMakeFiles/mdlib-test.dir/settletestdata.cpp.o CMakeFiles/mdlib-test.dir/settletestrunners.cpp.o CMakeFiles/mdlib-test.dir/shake.cpp.o CMakeFiles/mdlib-test.dir/simulationsignal.cpp.o CMakeFiles/mdlib-test.dir/updategroups.cpp.o CMakeFiles/mdlib-test.dir/updategroupscog.cpp.o CMakeFiles/mdlib-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdlib-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 73%] Built target mdlib-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/devicetransfers.cpp
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/CMakeFiles/math-test.dir/DependInfo.cmake --color=
Scanning dependencies of target math-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/math/tests/CMakeFiles/math-test.dir/build.make src/gromacs/math/tests/CMakeFiles/math-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/hardware/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/arrayrefwithpadding.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_AssignFromPaddedVectorWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::ArrayRefWithPaddingTest_ConstructFromPointersWorks_Test<gmx::ArrayRefWithPadding<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/hardware/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/hardware-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/hardware-test.dir/hardwaretopology.cpp.o CMakeFiles/hardware-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/hardware-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = double]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
In file included from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:57:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target hardware-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp: In function 'void gmx::test::runTest(const gmx_gpu_info_t&, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
100 | void runTest(const gmx_gpu_info_t& gpuInfo, ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:100:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_VectorsWithDefaultHostAllocatorAlwaysWorks_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::test::HostAllocatorTestCopyable_TransfersWithoutPinningWork_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::BasicVector<double>]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
206 | runTest(*this->gpuInfo_, makeArrayRef(input), makeArrayRef(output));
| ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gpu_utils/tests/hostallocator.cpp:206:12: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/keyvaluetreetransform.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinitytest.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_identityTransformation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:77:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
77 | translateAndScale(toBeTransformed);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationWithIdentityScaling_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:84:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
84 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingWithZeroTranslation_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:94:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
94 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_translationAndScalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:104:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | translateAndScale(testVectors_);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gpu_utils/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingIdentity_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:115:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
115 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingNonTrivial_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:125:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
125 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseNoZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:133:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
133 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:134:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
134 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp: In member function 'virtual void gmx::test::TranslateAndScaleTest_scalingInverseWithOneScaleDimensionZero_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:142:10: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
142 | scale(testVectors_);
| ~~~~~^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/coordinatetransformation.cpp:143:35: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | scale.inverseIgnoringZeroScale(testVectors_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gpu_utils/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gpu_utils-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gpu_utils-test.dir/gputest.cpp.o CMakeFiles/gpu_utils-test.dir/clfftinitializer.cpp.o CMakeFiles/gpu_utils-test.dir/hostallocator.cpp.o CMakeFiles/gpu_utils-test.dir/devicetransfers.cpp.o CMakeFiles/gpu_utils-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gpu_utils-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target gpu_utils-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/logger.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -P CMakeFiles/mdrunutility-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libmdrunutility-test-shared.a CMakeFiles/mdrunutility-test-shared.dir/threadaffinitytest.cpp.o
/usr/bin/ranlib ../../../../lib/libmdrunutility-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 75%] Built target mdrunutility-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/dofit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/dofit.cpp
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdspan-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build.make src/gromacs/mdspan/tests/CMakeFiles/mdspan-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/accessor_policy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/mutex.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/mutex.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extents.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extents.cpp
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/DependInfo.cmake --color=
Scanning dependencies of target onlinehelp-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build.make src/gromacs/onlinehelp/tests/CMakeFiles/onlinehelp-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpformat.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/extensions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/extensions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/path.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/layouts.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/layouts.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/tests/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/mdspan.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdspan/tests/mdspan.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/onlinehelp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/onlinehelp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/onlinehelp-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/onlinehelp-test.dir/helpformat.cpp.o CMakeFiles/onlinehelp-test.dir/helpmanager.cpp.o CMakeFiles/onlinehelp-test.dir/helpwritercontext.cpp.o CMakeFiles/onlinehelp-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/onlinehelp-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 76%] Built target onlinehelp-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textreader.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/functions.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_ErfInvDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_SixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsqrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvcbrtDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootDouble_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::FunctionTest_InvsixthrootInteger_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/densityfittingforce.cpp
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/CMakeFiles/options-test.dir/DependInfo.cmake --color=
Scanning dependencies of target options-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/options/tests/CMakeFiles/options-test.dir/build.make src/gromacs/options/tests/CMakeFiles/options-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/abstractoptionstorage.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/typetraits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/tests/typetraits.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdspan/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/matrix.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/utility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdspan/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdspan-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdspan-test.dir/accessor_policy.cpp.o CMakeFiles/mdspan-test.dir/extents.cpp.o CMakeFiles/mdspan-test.dir/extensions.cpp.o CMakeFiles/mdspan-test.dir/layouts.cpp.o CMakeFiles/mdspan-test.dir/mdspan.cpp.o CMakeFiles/mdspan-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdspan-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 77%] Built target mdspan-test
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pbcutil-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build.make src/gromacs/pbcutil/tests/CMakeFiles/pbcutil-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbc.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/utility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/utility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/utility-test.dir/alignedallocator.cpp.o CMakeFiles/utility-test.dir/arrayref.cpp.o CMakeFiles/utility-test.dir/bitmask32.cpp.o CMakeFiles/utility-test.dir/bitmask64.cpp.o CMakeFiles/utility-test.dir/bitmask128.cpp.o CMakeFiles/utility-test.dir/cstringutil.cpp.o CMakeFiles/utility-test.dir/defaultinitializationallocator.cpp.o CMakeFiles/utility-test.dir/enumerationhelpers.cpp.o CMakeFiles/utility-test.dir/fixedcapacityvector.cpp.o CMakeFiles/utility-test.dir/inmemoryserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreeserializer.cpp.o CMakeFiles/utility-test.dir/keyvaluetreetransform.cpp.o CMakeFiles/utility-test.dir/logger.cpp.o CMakeFiles/utility-test.dir/mutex.cpp.o CMakeFiles/utility-test.dir/path.cpp.o CMakeFiles/utility-test.dir/physicalnodecommunicator.cpp.o CMakeFiles/utility-test.dir/stringutil.cpp.o CMakeFiles/utility-test.dir/textreader.cpp.o CMakeFiles/utility-test.dir/textwriter.cpp.o CMakeFiles/utility-test.dir/typetraits.cpp.o CMakeFiles/utility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/utility-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target utility-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/tests/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pbcutil/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/multidimarray.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/multidimarray.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pbcutil/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pbcutil-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pbcutil-test.dir/pbc.cpp.o CMakeFiles/pbcutil-test.dir/pbcenums.cpp.o CMakeFiles/pbcutil-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pbcutil-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target pbcutil-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/filenameoptionmanager.cpp
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/CMakeFiles/random-test.dir/DependInfo.cmake --color=
Scanning dependencies of target random-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/random/tests/CMakeFiles/random-test.dir/build.make src/gromacs/random/tests/CMakeFiles/random-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/exponentialdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/DependInfo.cmake --color=
Scanning dependencies of target restraintpotential-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build.make src/gromacs/restraint/tests/CMakeFiles/restraintpotential-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/tests/manager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/restraint/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/exponentialdistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ExponentialDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/restraint/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/restraintpotential-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/restraintpotential-test.dir/manager.cpp.o CMakeFiles/restraintpotential-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/restraintpotential-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target restraintpotential-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/gammadistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/paddedvector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/CMakeFiles/table-test.dir/DependInfo.cmake --color=
Scanning dependencies of target table-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tables/tests/CMakeFiles/table-test.dir/build.make src/gromacs/tables/tests/CMakeFiles/table-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/splinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/gammadistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::GammaDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/option.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/option.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/normaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/optionsassigner.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/normaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::NormalDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_NumericalInputPmeCorr_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:515:15: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
515 | TypeParam pmeCorrTable({ { "NumericalPMECorr", functionValues, derivativeValues, inputSpacing } },
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/seed.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::QuadraticSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp: In member function 'void gmx::test::{anonymous}::SplineTableTest_HandlesIncorrectNumericalInput_Test<gtest_TypeParam_>::TestBody() [with gtest_TypeParam_ = gmx::CubicSplineTable]':
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:457:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
457 | TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.001 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:456:5: note: in expansion of macro 'EXPECT_THROW_GMX'
456 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:463:5: note: in expansion of macro 'EXPECT_THROW_GMX'
463 | EXPECT_THROW_GMX(TypeParam({ { "EmptyVectors", functionValues, derivativeValues, 0.1 } }, { 1.0, 2.0 }),
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:58,
from /<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:50:
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:22: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
486 | { 0.2, 1.0 }),
| ~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:485:5: note: in expansion of macro 'EXPECT_THROW_GMX'
485 | EXPECT_THROW_GMX(TypeParam({ { "NumericalBadLJ12", functionValues, badDerivativeValues, spacing } },
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:492:13: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
492 | TypeParam({ { "NumericalLJ12", functionValues, derivativeValues, spacing } }, { 0.2, 1.0 }),
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/testutils/testasserts.h:191:5: note: in expansion of macro 'GMX_TEST_THROW_'
191 | GMX_TEST_THROW_(statement, expected_exception, GTEST_NONFATAL_FAILURE_)
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/tests/splinetable.cpp:491:5: note: in expansion of macro 'EXPECT_THROW_GMX'
491 | EXPECT_THROW_GMX(
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp
In file included from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:59:
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::fillInputContents(gmx::ArrayRef<gmx::BasicVector<ValueType> >, int) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:69:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
69 | void fillInputContents(ArrayRef<BasicVector<T>> inputRef, int scaleFactor)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
94 | void compareViews(ArrayRef<T> input, ArrayRef<T> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:94:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h: In function 'void gmx::test::compareViews(gmx::ArrayRef<gmx::BasicVector<ValueType> >, gmx::ArrayRef<gmx::BasicVector<ValueType> >) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
105 | void compareViews(ArrayRef<BasicVector<T>> input, ArrayRef<BasicVector<T>> output)
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/tests/testarrayrefs.h:105:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/tabulatednormaldistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::TabulatedNormalDistributionTest_OutputDouble14_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, std::allocator<double> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/threefry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tables/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tables/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/table-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/table-test.dir/splinetable.cpp.o CMakeFiles/table-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/table-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target table-test
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/DependInfo.cmake --color=
Scanning dependencies of target taskassignment-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build.make src/gromacs/taskassignment/tests/CMakeFiles/taskassignment-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/tests/usergpuids.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'std::vector<_Tp, _Alloc>::vector(std::initializer_list<_Tp>, const allocator_type&) [with _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/stl_vector.h:625:7: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
625 | vector(initializer_list<value_type> __l,
| ^~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/repeatingsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/repeatingsection.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/math/tests/paddedvector.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::test::fillInput(PaddedVectorOfT*, int) [with PaddedVectorOfT = gmx::PaddedVector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, std::allocator<gmx::BasicVector<double> > > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /usr/include/c++/10/bits/random.h:34,
from /usr/include/c++/10/random:49,
from /<<PKGBUILDDIR>>/src/gromacs/random/seed.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/threefry.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {long long unsigned int}; _Tp = long long unsigned int; _Alloc = std::allocator<long long unsigned int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long unsigned int>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_InternalCounterSequence_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Default_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Using40Rounds_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::ThreeFry2x64Test_Fast_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long unsigned int*, std::vector<long long unsigned int> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:117:54: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
117 | const std::vector<uint64_t> bitsZero{ { 0, 0, 0, 0 } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:127:87: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
127 | 0xFFFFFFFFFFFFFFFFULL, 0xFFFFFFFFFFFFFFFFULL } };
| ^
/<<PKGBUILDDIR>>/src/gromacs/random/tests/threefry.cpp:136:86: note: parameter passing for argument of type 'std::initializer_list<long long unsigned int>' changed in GCC 7.1
136 | 0xa4093822299f31d0ULL, 0x082efa98ec4e6c89ULL } };
| ^
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/vectypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/tests/vectypes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformintdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/taskassignment/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/taskassignment/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/taskassignment-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/taskassignment-test.dir/usergpuids.cpp.o CMakeFiles/taskassignment-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/taskassignment-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 78%] Built target taskassignment-test
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/CMakeFiles/topology-test.dir/DependInfo.cmake --color=
Scanning dependencies of target topology-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build.make src/gromacs/topology/tests/CMakeFiles/topology-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/math/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/mtop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/mtop.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/random/tests/uniformrealdistribution.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_GenerateCanonical_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::UniformRealDistributionTest_Output_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/math/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/math-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/math-test.dir/arrayrefwithpadding.cpp.o CMakeFiles/math-test.dir/coordinatetransformation.cpp.o CMakeFiles/math-test.dir/densityfit.cpp.o CMakeFiles/math-test.dir/dofit.cpp.o CMakeFiles/math-test.dir/exponentialmovingaverage.cpp.o CMakeFiles/math-test.dir/functions.cpp.o CMakeFiles/math-test.dir/gausstransform.cpp.o CMakeFiles/math-test.dir/densityfittingforce.cpp.o CMakeFiles/math-test.dir/invertmatrix.cpp.o CMakeFiles/math-test.dir/matrix.cpp.o CMakeFiles/math-test.dir/multidimarray.cpp.o CMakeFiles/math-test.dir/paddedvector.cpp.o CMakeFiles/math-test.dir/vectypes.cpp.o CMakeFiles/math-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/math-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 79%] Built target math-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/tests/symtab.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/random/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/tests/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/topology/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/random/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/random-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/random-test.dir/exponentialdistribution.cpp.o CMakeFiles/random-test.dir/gammadistribution.cpp.o CMakeFiles/random-test.dir/normaldistribution.cpp.o CMakeFiles/random-test.dir/seed.cpp.o CMakeFiles/random-test.dir/tabulatednormaldistribution.cpp.o CMakeFiles/random-test.dir/threefry.cpp.o CMakeFiles/random-test.dir/uniformintdistribution.cpp.o CMakeFiles/random-test.dir/uniformrealdistribution.cpp.o CMakeFiles/random-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/random-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target random-test
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pull-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build.make src/gromacs/pulling/tests/CMakeFiles/pull-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/tests/pull.cpp
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/CMakeFiles/awh-test.dir/DependInfo.cmake --color=
Scanning dependencies of target awh-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build.make src/gromacs/awh/tests/CMakeFiles/awh-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/pulling/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/topology/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/topology-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/topology-test.dir/exclusionblocks.cpp.o CMakeFiles/topology-test.dir/mtop.cpp.o CMakeFiles/topology-test.dir/symtab.cpp.o CMakeFiles/topology-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/topology-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target topology-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/options/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/pulling/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pull-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pull-test.dir/pull.cpp.o CMakeFiles/pull-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pull-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 80%] Built target pull-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::test::AwhTestParameters gmx::test::getAwhTestParameters(int, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::test::BiasTest_ForcesBiasPmf_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/bias.cpp:37:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/grid.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, double, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::test::gridTest_neighborhood_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/awh/tests/biasstate.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double, double, double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::test::BiasStateTest::BiasStateTest()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/CMakeFiles/simd-test.dir/DependInfo.cmake --color=
Scanning dependencies of target simd-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build.make src/gromacs/simd/tests/CMakeFiles/simd-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/bootstrap_loadstore.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/options/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/options-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/options-test.dir/abstractoptionstorage.cpp.o CMakeFiles/options-test.dir/filenameoption.cpp.o CMakeFiles/options-test.dir/filenameoptionmanager.cpp.o CMakeFiles/options-test.dir/option.cpp.o CMakeFiles/options-test.dir/optionsassigner.cpp.o CMakeFiles/options-test.dir/repeatingsection.cpp.o CMakeFiles/options-test.dir/timeunitmanager.cpp.o CMakeFiles/options-test.dir/treesupport.cpp.o CMakeFiles/options-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/options-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/base.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/base.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target options-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/awh/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/CMakeFiles/compat-test.dir/DependInfo.cmake --color=
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/DependInfo.cmake --color=
Scanning dependencies of target compat-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build.make src/gromacs/compat/tests/CMakeFiles/compat-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-unused-member-function -o CMakeFiles/compat-test.dir/optional.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/optional.cpp
Scanning dependencies of target gmxana-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build.make src/gromacs/gmxana/tests/CMakeFiles/gmxana-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/entropy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/awh/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/awh-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/awh-test.dir/bias.cpp.o CMakeFiles/awh-test.dir/biasstate.cpp.o CMakeFiles/awh-test.dir/grid.cpp.o CMakeFiles/awh-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/awh-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 81%] Built target awh-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/thermochemistry.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/entropy.cpp:43:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::{anonymous}::Entropy::runQuasiHarmonic(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::{anonymous}::Entropy::runSchlitter(real, gmx_bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_traj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_mindist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_floatingpoint_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxana/tests/gmx_msd.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/pointers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/pointers.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxana/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_memory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_memory.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/string_view.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/compat/tests/string_view.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxana-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxana-test.dir/entropy.cpp.o CMakeFiles/gmxana-test.dir/gmx_traj.cpp.o CMakeFiles/gmxana-test.dir/gmx_mindist.cpp.o CMakeFiles/gmxana-test.dir/gmx_msd.cpp.o CMakeFiles/gmxana-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxana-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd_integer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd_integer.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target gmxana-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/compat/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_floatingpoint.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx3-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx3-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_vector_operations.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/simd4_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/simd4_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_util.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/scalar_math.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/tests/scalar_math.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=1 -DCHARMM=1 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx2-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx2-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx3-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx3-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx3-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx3-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target pdb2gmx3-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=1 -DHAVE_CONFIG_H -DOPLSAA=0 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/simd/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/compat/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/compat-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/compat-test.dir/optional.cpp.o CMakeFiles/compat-test.dir/pointers.cpp.o CMakeFiles/compat-test.dir/string_view.cpp.o CMakeFiles/compat-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/compat-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/DependInfo.cmake --color=
Scanning dependencies of target pdb2gmx1-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/pdb2gmx1-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/pdb2gmx.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 82%] Built target compat-test
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxpreprocess-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build.make src/gromacs/gmxpreprocess/tests/CMakeFiles/gmxpreprocess-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/editconf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/simd/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/simd-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/simd-test.dir/bootstrap_loadstore.cpp.o CMakeFiles/simd-test.dir/base.cpp.o CMakeFiles/simd-test.dir/simd.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd_floatingpoint_util.cpp.o CMakeFiles/simd-test.dir/simd_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd_math.cpp.o CMakeFiles/simd-test.dir/simd_memory.cpp.o CMakeFiles/simd-test.dir/simd_integer.cpp.o CMakeFiles/simd-test.dir/simd4.cpp.o CMakeFiles/simd-test.dir/simd4_floatingpoint.cpp.o CMakeFiles/simd-test.dir/simd4_vector_operations.cpp.o CMakeFiles/simd-test.dir/simd4_math.cpp.o CMakeFiles/simd-test.dir/scalar.cpp.o CMakeFiles/simd-test.dir/scalar_util.cpp.o CMakeFiles/simd-test.dir/scalar_math.cpp.o CMakeFiles/simd-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/simd-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 84%] Built target simd-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genconf.cpp
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/DependInfo.cmake --color=
Scanning dependencies of target correlations-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build.make src/gromacs/correlationfunctions/tests/CMakeFiles/correlations-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/autocorr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genion.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/autocorr.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/autocorr.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacVector_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP2_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP3_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP4_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP1_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacRcross_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacP0_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNormal_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacNoNormalize_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void gmx::{anonymous}::AutocorrTest_EacCos_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/manyautocorrelation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/genrestr.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx2-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx2-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx2-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx2-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target pdb2gmx2-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/correlationdataset.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/expfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DAMBER=0 -DCHARMM=0 -DGMX_DOUBLE=1 -DGROMOS=0 -DHAVE_CONFIG_H -DOPLSAA=1 -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_bond_atomtype.cpp
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_IndexOutOfRangeInvalid_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_NoNameFromIncorrectTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFromTypeNumber_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_WrongNameNotFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CorrectNameFound_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddTypeWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_EmptyOnCreate_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_AddMultipleTypesWorks_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp: In member function 'testing::Test* testing::internal::TestFactoryImpl<TestClass>::CreateTest() [with TestClass = gmx::{anonymous}::PreprocessingAtomTypesTest_CannotAddDuplicateEntry_Test]':
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
61 | PreprocessingAtomTypesTest() : nb_({}, {}) { open_symtab(&symtab_); }
| ^
/<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/gpp_atomtype.cpp:61:46: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/pdb2gmx1-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/pdb2gmx1-test.dir/pdb2gmx.cpp.o CMakeFiles/pdb2gmx1-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/pdb2gmx1-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 85%] Built target pdb2gmx1-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/correlationfunctions/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/external/googletest/googletest/include/gtest/gtest.h:56,
from /<<PKGBUILDDIR>>/src/gromacs/correlationfunctions/tests/expfit.cpp:51:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In static member function 'static void gmx::{anonymous}::ExpfitTest::SetUpTestCase()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test-shared
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test-shared.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target coordinateio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build.make src/gromacs/coordinateio/tests/CMakeFiles/coordinateio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/builder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/builder.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/correlationfunctions/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/correlations-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/correlations-test.dir/autocorr.cpp.o CMakeFiles/correlations-test.dir/manyautocorrelation.cpp.o CMakeFiles/correlations-test.dir/correlationdataset.cpp.o CMakeFiles/correlations-test.dir/expfit.cpp.o CMakeFiles/correlations-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/correlations-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target correlations-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadaptercontainer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/insert_molecules.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/datatest.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&}; _Tp = gmx::test::AnalysisDataTestInputPointSet::Value; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputPointSet::Value>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputPointSet::Value>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValueAndError(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInputFrame::addPointSetWithValues(int, int, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/DependInfo.cmake --color=
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::test::AnalysisDataTestInputFrame}; _Tp = gmx::test::AnalysisDataTestInputFrame; _Alloc = std::allocator<gmx::test::AnalysisDataTestInputFrame>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::test::AnalysisDataTestInputFrame>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
Scanning dependencies of target energyanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build.make src/gromacs/energyanalysis/tests/CMakeFiles/energyanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/legacyenergy.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::test::AnalysisDataTestInputFrame& gmx::test::AnalysisDataTestInput::addFrame(real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputFrame*, std::vector<gmx::test::AnalysisDataTestInputFrame> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValues(real, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::test::AnalysisDataTestInput::addFrameWithValueAndError(real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::test::AnalysisDataTestInputPointSet::Value*, std::vector<gmx::test::AnalysisDataTestInputPointSet::Value> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/mock_datamodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/readir.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/energyanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/outputadapters.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/energyanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/energyanalysis-test.dir/legacyenergy.cpp.o CMakeFiles/energyanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/energyanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 86%] Built target energyanalysis-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/requirements.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/requirements.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/solvate.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/topdirs.cpp
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/CMakeFiles/tool-test.dir/DependInfo.cmake --color=
Scanning dependencies of target tool-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build.make src/gromacs/tools/tests/CMakeFiles/tool-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/dump.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/gmxpreprocess/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/report_methods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/report_methods.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxpreprocess-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxpreprocess-test.dir/editconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genconf.cpp.o CMakeFiles/gmxpreprocess-test.dir/genion.cpp.o CMakeFiles/gmxpreprocess-test.dir/genrestr.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/gpp_bond_atomtype.cpp.o CMakeFiles/gmxpreprocess-test.dir/insert_molecules.cpp.o CMakeFiles/gmxpreprocess-test.dir/readir.cpp.o CMakeFiles/gmxpreprocess-test.dir/solvate.cpp.o CMakeFiles/gmxpreprocess-test.dir/topdirs.cpp.o CMakeFiles/gmxpreprocess-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/gmxpreprocess-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target gmxpreprocess-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setatoms.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/trjconv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tools/tests/trjconv.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -P CMakeFiles/analysisdata-test-shared.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test-shared.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libanalysisdata-test-shared.a CMakeFiles/analysisdata-test-shared.dir/datatest.cpp.o CMakeFiles/analysisdata-test-shared.dir/mock_datamodule.cpp.o
/usr/bin/ranlib ../../../../lib/libanalysisdata-test-shared.a
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 87%] Built target analysisdata-test-shared
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/tools/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/DependInfo.cmake --color=
Scanning dependencies of target fileio-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build.make src/gromacs/fileio/tests/CMakeFiles/fileio-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setbothtime.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/confio.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int, int, int}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'testing::Test* testing::internal::ParameterizedTestFactory<TestClass>::CreateTest() [with TestClass = {anonymous}::StructureIORoundtripTest_ReadWriteTpsConf_Test]':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/setstarttime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/filemd5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/filemd5.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/tool-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/tool-test.dir/dump.cpp.o CMakeFiles/tool-test.dir/report_methods.cpp.o CMakeFiles/tool-test.dir/trjconv.cpp.o CMakeFiles/tool-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/tool-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/settimestep.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 88%] Built target tool-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/coordinateio/tests/testmodule.cpp
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/CMakeFiles/selection-test.dir/DependInfo.cmake --color=
Scanning dependencies of target selection-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build.make src/gromacs/selection/tests/CMakeFiles/selection-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/coordinateio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/coordinateio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/coordinateio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/coordinateio-test.dir/builder.cpp.o CMakeFiles/coordinateio-test.dir/outputadaptercontainer.cpp.o CMakeFiles/coordinateio-test.dir/outputadapters.cpp.o CMakeFiles/coordinateio-test.dir/requirements.cpp.o CMakeFiles/coordinateio-test.dir/setatoms.cpp.o CMakeFiles/coordinateio-test.dir/setbothtime.cpp.o CMakeFiles/coordinateio-test.dir/setstarttime.cpp.o CMakeFiles/coordinateio-test.dir/settimestep.cpp.o CMakeFiles/coordinateio-test.dir/testmodule.cpp.o CMakeFiles/coordinateio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/coordinateio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target coordinateio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const {anonymous}::NeighborhoodSearchTestData::RefPair&}; _Tp = {anonymous}::NeighborhoodSearchTestData::RefPair; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::RefPair>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::NeighborhoodSearchTestData::computeReferencesInternal(t_pbc*, bool)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double*&}; _Tp = {anonymous}::NeighborhoodSearchTestData::TestPosition; _Alloc = std::allocator<{anonymous}::NeighborhoodSearchTestData::TestPosition>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTestData::useRefPositionsAsTestPositions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-modules-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-modules-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/densityfittingmodule.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double (&)[3]}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'gmx::AnalysisNeighborhoodPositions {anonymous}::NeighborhoodSearchTestData::testPositions() const':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTest::testPairSearch(gmx::AnalysisNeighborhoodSearch*, const {anonymous}::NeighborhoodSearchTestData&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp: In member function 'virtual void gmx::test::{anonymous}::MrcDensityMap_ReadsCoordinateTransformationFromFile_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:110:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
110 | coordinateTransformation({ &coordinate1, &coordinate1 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymap.cpp:111:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
111 | coordinateTransformation({ &coordinate2, &coordinate2 + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::BasicVector<double>}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void {anonymous}::NeighborhoodSearchTest::testPairSearchIndexed(gmx::AnalysisNeighborhood*, const {anonymous}::NeighborhoodSearchTestData&, uint64_t)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomTestPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::TestPosition*, std::vector<{anonymous}::NeighborhoodSearchTestData::TestPosition> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void {anonymous}::NeighborhoodSearchTestData::generateRandomRefPositions(int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-test
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h: In static member function 'static const {anonymous}::NeighborhoodSearchTestData& {anonymous}::RandomBoxXYFullPBCData::get()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/domain_decomposition.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchTriclinic_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearch2DPBC_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearch_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/interactiveMD.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_GridSearchBox_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSearchExclusions_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesSkippingPairs_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_SimpleSelfPairsSearch_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesConcurrentSearches_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<{anonymous}::NeighborhoodSearchTestData::RefPair*, std::vector<{anonymous}::NeighborhoodSearchTestData::RefPair> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/selection/tests/nbsearch.cpp:49:
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNullPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'virtual void {anonymous}::NeighborhoodSearchTest_HandlesNoPBC_Test::TestBody()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/poscalc.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformNoOriginGiven_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:87:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
87 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithOriginDefined_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:106:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp: In member function 'virtual void gmx::MrcDensityMapHeaderTest_GetsCorrectCoordinateTransformWithStartValues_Test::TestBody()':
/<<PKGBUILDDIR>>/src/gromacs/fileio/tests/mrcdensitymapheader.cpp:124:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
124 | getCoordinateTransformationToLattice(header)(testVectors);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/readinp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/fileioxdrserializer.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-modules-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-modules-test.dir/densityfittingmodule.cpp.o CMakeFiles/mdrun-modules-test.dir/interactiveMD.cpp.o CMakeFiles/mdrun-modules-test.dir/mimic.cpp.o CMakeFiles/mdrun-modules-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-modules-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 89%] Built target mdrun-modules-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tests/tngio.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/mimic.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/fileio/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/fileio/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/fileio-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/fileio-test.dir/confio.cpp.o CMakeFiles/fileio-test.dir/filemd5.cpp.o CMakeFiles/fileio-test.dir/mrcserializer.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymap.cpp.o CMakeFiles/fileio-test.dir/mrcdensitymapheader.cpp.o CMakeFiles/fileio-test.dir/readinp.cpp.o CMakeFiles/fileio-test.dir/fileioxdrserializer.cpp.o CMakeFiles/fileio-test.dir/tngio.cpp.o CMakeFiles/fileio-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/fileio-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target fileio-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisim.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-mpi-coordination-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-mpi-coordination-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/periodicactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/multisimtest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-coordination-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-coordination-test.dir/periodicactions.cpp.o CMakeFiles/mdrun-mpi-coordination-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-coordination-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/replicaexchange.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 90%] Built target mdrun-mpi-coordination-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/toputils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/tests/toputils.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-io-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-io-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/exactcontinuation.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/dispersion_correction.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/orires.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/orires.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/pmetest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/pmetest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/selection/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-mpi-test.dir/domain_decomposition.cpp.o CMakeFiles/mdrun-mpi-test.dir/minimize.cpp.o CMakeFiles/mdrun-mpi-test.dir/mimic.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisim.cpp.o CMakeFiles/mdrun-mpi-test.dir/multisimtest.cpp.o CMakeFiles/mdrun-mpi-test.dir/pmetest.cpp.o CMakeFiles/mdrun-mpi-test.dir/replicaexchange.cpp.o CMakeFiles/mdrun-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target mdrun-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/grompp.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/selection/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/selection-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/selection-test.dir/indexutil.cpp.o CMakeFiles/selection-test.dir/nbsearch.cpp.o CMakeFiles/selection-test.dir/poscalc.cpp.o CMakeFiles/selection-test.dir/selectioncollection.cpp.o CMakeFiles/selection-test.dir/selectionoption.cpp.o CMakeFiles/selection-test.dir/toputils.cpp.o CMakeFiles/selection-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/selection-test ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 ../../../../lib/libgmock.so -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 91%] Built target selection-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/simulator.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simulator.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-output-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-output-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/compressed_x_output.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/initialconstraints.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/termination.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/termination.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/helpwriting.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/outputfiles.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/swapcoords.cpp
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-non-integrator-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-non-integrator-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/minimize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tabulated_bonded_interactions.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-io-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-io-test.dir/exactcontinuation.cpp.o CMakeFiles/mdrun-io-test.dir/grompp.cpp.o CMakeFiles/mdrun-io-test.dir/initialconstraints.cpp.o CMakeFiles/mdrun-io-test.dir/termination.cpp.o CMakeFiles/mdrun-io-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-io-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 92%] Built target mdrun-io-test
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun-tpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build.make src/programs/mdrun/tests/CMakeFiles/mdrun-tpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/tpitest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-test.dir/dispersion_correction.cpp.o CMakeFiles/mdrun-test.dir/orires.cpp.o CMakeFiles/mdrun-test.dir/pmetest.cpp.o CMakeFiles/mdrun-test.dir/simulator.cpp.o CMakeFiles/mdrun-test.dir/swapcoords.cpp.o CMakeFiles/mdrun-test.dir/tabulated_bonded_interactions.cpp.o CMakeFiles/mdrun-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/nonbonded_bench.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-tpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-tpi-test.dir/tpitest.cpp.o CMakeFiles/mdrun-tpi-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-tpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 93%] Built target mdrun-tpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/normalmodes.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-output-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-output-test.dir/compressed_x_output.cpp.o CMakeFiles/mdrun-output-test.dir/helpwriting.cpp.o CMakeFiles/mdrun-output-test.dir/outputfiles.cpp.o CMakeFiles/mdrun-output-test.dir/trajectory_writing.cpp.o CMakeFiles/mdrun-output-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-output-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target mdrun-output-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target gmxapi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build.make src/api/cpp/tests/CMakeFiles/gmxapi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/restraint.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/restraint.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/status.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/status.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/system.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/system.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-mpi-test.dir/workflow.cpp.o CMakeFiles/workflow-details-mpi-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-mpi-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 94%] Built target workflow-details-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/version.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/version.cpp
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/DependInfo.cmake --color=
Scanning dependencies of target workflow-details-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build.make src/api/cpp/workflow/tests/CMakeFiles/workflow-details-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/workflow.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/workflow/tests/workflow.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/rerun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/runner.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/runner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/workflow/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -I/<<PKGBUILDDIR>>/src/api/cpp -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/workflow-details-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/workflow-details-test.dir/workflow.cpp.o CMakeFiles/workflow-details-test.dir/__/__/__/__/testutils/unittest_main.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../../bin/workflow-details-test ../../../../../lib/libtestutils.a ../../../../../lib/libgmxapi_d.so.0.1.0 ../../../../../lib/libmdrun_test_infrastructure.a ../../../../../lib/libtestutils.a ../../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../../lib/libgmock.so ../../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target workflow-details-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/api/cpp/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/api/cpp/tests -I/<<PKGBUILDDIR>>/src/api/cpp/include -I/<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/include -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o -c /<<PKGBUILDDIR>>/src/api/cpp/tests/stopsignaler.cpp
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/DependInfo.cmake --color=
Scanning dependencies of target commandline-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build.make src/gromacs/commandline/tests/CMakeFiles/commandline-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-mpi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-mpi-test.dir/status.cpp.o CMakeFiles/gmxapi-mpi-test.dir/system.cpp.o CMakeFiles/gmxapi-mpi-test.dir/version.cpp.o CMakeFiles/gmxapi-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-mpi-test.dir/runner.cpp.o CMakeFiles/gmxapi-mpi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 95%] Built target gmxapi-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/tests/simple_mdrun.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/programs/mdrun/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-mpi-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-mpi-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity_mpi.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/gmxapi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/gmxapi-test.dir/restraint.cpp.o CMakeFiles/gmxapi-test.dir/status.cpp.o CMakeFiles/gmxapi-test.dir/system.cpp.o CMakeFiles/gmxapi-test.dir/version.cpp.o CMakeFiles/gmxapi-test.dir/__/__/__/testutils/unittest_main.cpp.o CMakeFiles/gmxapi-test.dir/runner.cpp.o CMakeFiles/gmxapi-test.dir/stopsignaler.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../../programs/CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/gmxapi-test ../../../../lib/libtestutils.a ../../../../lib/libgmxapi_d.so.0.1.0 ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target gmxapi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -DTEST_USES_MPI=true -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlinemodulemanagertest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-mpi-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-mpi-test.dir/threadaffinity_mpi.cpp.o CMakeFiles/mdrunutility-mpi-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-mpi-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrunutility-mpi-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun-non-integrator-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun-non-integrator-test.dir/minimize.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/nonbonded_bench.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/normalmodes.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/rerun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/simple_mdrun.cpp.o CMakeFiles/mdrun-non-integrator-test.dir/__/__/__/testutils/unittest_main.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o ../../CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../../../bin/mdrun-non-integrator-test ../../../../lib/libtestutils.a ../../../../lib/libmdrun_test_infrastructure.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrun-non-integrator-test
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrunutility-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build.make src/gromacs/mdrunutility/tests/CMakeFiles/mdrunutility-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/tests/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/cmdlineprogramcontext.cpp
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/DependInfo.cmake --color=
Scanning dependencies of target analysisdata-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build.make src/gromacs/analysisdata/tests/CMakeFiles/analysisdata-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/analysisdata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/filenm.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/mdrunutility/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/tests/pargs.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdrunutility/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrunutility-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrunutility-test.dir/threadaffinity.cpp.o CMakeFiles/mdrunutility-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/mdrunutility-test ../../../../lib/libtestutils.a ../../../../lib/libmdrunutility-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 96%] Built target mdrunutility-test
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/DependInfo.cmake --color=
Scanning dependencies of target trajectoryanalysis-test
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build.make src/gromacs/trajectoryanalysis/tests/CMakeFiles/trajectoryanalysis-test.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/moduletest.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/arraydata.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/cmdlinerunner.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/commandline/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/angle.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/commandline/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/commandline-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/commandline-test.dir/cmdlinehelpmodule.cpp.o CMakeFiles/commandline-test.dir/cmdlinehelpwriter.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanager.cpp.o CMakeFiles/commandline-test.dir/cmdlinemodulemanagertest.cpp.o CMakeFiles/commandline-test.dir/cmdlineparser.cpp.o CMakeFiles/commandline-test.dir/cmdlineprogramcontext.cpp.o CMakeFiles/commandline-test.dir/filenm.cpp.o CMakeFiles/commandline-test.dir/pargs.cpp.o CMakeFiles/commandline-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/commandline-test ../../../../lib/libtestutils.a ../../../../lib/libonlinehelp-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target commandline-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/average.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/average.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/histogram.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/histogram.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/convert_trj.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/distance.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/extract_cluster.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/pairdist.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/rdf.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/sasa.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/analysisdata/tests/lifetime.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/analysisdata/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/select.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/topologyinformation.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/analysisdata/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/analysisdata-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/analysisdata-test.dir/analysisdata.cpp.o CMakeFiles/analysisdata-test.dir/arraydata.cpp.o CMakeFiles/analysisdata-test.dir/average.cpp.o CMakeFiles/analysisdata-test.dir/histogram.cpp.o CMakeFiles/analysisdata-test.dir/lifetime.cpp.o CMakeFiles/analysisdata-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/analysisdata-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/trajectory.cpp
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[ 97%] Built target analysisdata-test
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/unionfind.cpp
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/c++ -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DTEST_DATA_PATH=\"src/gromacs/trajectoryanalysis/tests\" -DTEST_TEMP_PATH=\"/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary\" -I/<<PKGBUILDDIR>>/build/basic-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/googletest/googlemock/include -isystem /<<PKGBUILDDIR>>/src/external/googletest/googletest/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -c /<<PKGBUILDDIR>>/src/testutils/unittest_main.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/modules/surfacearea.h:41,
from /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/surfacearea.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void {anonymous}::SurfaceAreaTest::generateRandomPositions(int)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesSinglePoint_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPoints_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_ComputesTwoPointsOfUnequalRadius_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints12_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints32_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints42_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void {anonymous}::SurfaceAreaTest_SurfacePoints122_Test::TestBody()':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/trajectoryanalysis-test.dir/link.txt --verbose=1
/usr/bin/c++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/trajectoryanalysis-test.dir/moduletest.cpp.o CMakeFiles/trajectoryanalysis-test.dir/clustsize.cpp.o CMakeFiles/trajectoryanalysis-test.dir/cmdlinerunner.cpp.o CMakeFiles/trajectoryanalysis-test.dir/angle.cpp.o CMakeFiles/trajectoryanalysis-test.dir/convert_trj.cpp.o CMakeFiles/trajectoryanalysis-test.dir/distance.cpp.o CMakeFiles/trajectoryanalysis-test.dir/extract_cluster.cpp.o CMakeFiles/trajectoryanalysis-test.dir/freevolume.cpp.o CMakeFiles/trajectoryanalysis-test.dir/pairdist.cpp.o CMakeFiles/trajectoryanalysis-test.dir/rdf.cpp.o CMakeFiles/trajectoryanalysis-test.dir/sasa.cpp.o CMakeFiles/trajectoryanalysis-test.dir/select.cpp.o CMakeFiles/trajectoryanalysis-test.dir/surfacearea.cpp.o CMakeFiles/trajectoryanalysis-test.dir/topologyinformation.cpp.o CMakeFiles/trajectoryanalysis-test.dir/trajectory.cpp.o CMakeFiles/trajectoryanalysis-test.dir/unionfind.cpp.o CMakeFiles/trajectoryanalysis-test.dir/__/__/__/testutils/unittest_main.cpp.o -o ../../../../bin/trajectoryanalysis-test ../../../../lib/libtestutils.a ../../../../lib/libanalysisdata-test-shared.a ../../../../lib/libtestutils.a ../../../../lib/libgromacs_d.so.5.0.0 -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so ../../../../lib/libgmock.so ../../../../lib/libgtest.so -lpthread
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target trajectoryanalysis-test
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/depend
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
cd /<<PKGBUILDDIR>>/build/basic-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles/tests.dir/DependInfo.cmake --color=
Scanning dependencies of target tests
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/make -f CMakeFiles/tests.dir/build.make CMakeFiles/tests.dir/build
make[4]: Entering directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[4]: Nothing to be done for 'CMakeFiles/tests.dir/build'.
make[4]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
[100%] Built target tests
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/basic-dp/CMakeFiles 0
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/basic-dp'
(cd build/basic-dp; LD_LIBRARY_PATH=/<<PKGBUILDDIR>>/build/basic-dp/lib ctest -V || dpkg-architecture -i hurd-i386 || dpkg-architecture -i i386 )
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
UpdateCTestConfiguration from :/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Parse Config file:/<<PKGBUILDDIR>>/build/basic-dp/DartConfiguration.tcl
Test project /<<PKGBUILDDIR>>/build/basic-dp
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
Checking test dependency graph end
test 1
Start 1: TestUtilsUnitTests
1: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsUnitTests.xml"
1: Test timeout computed to be: 30
1: [==========] Running 59 tests from 5 test cases.
1: [----------] Global test environment set-up.
1: [----------] 10 tests from InteractiveTestHelperTest
1: [ RUN ] InteractiveTestHelperTest.ChecksSimpleSession
1: [ OK ] InteractiveTestHelperTest.ChecksSimpleSession (3 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithoutLastNewline (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput
1: [ OK ] InteractiveTestHelperTest.ChecksSessionWithEquivalentOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsIncorrectOutput
1: [ OK ] InteractiveTestHelperTest.DetectsIncorrectOutput (3 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingFinalOutput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingFinalOutput (1 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraOutput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraOutput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsMissingInput
1: [ OK ] InteractiveTestHelperTest.DetectsMissingInput (2 ms)
1: [ RUN ] InteractiveTestHelperTest.DetectsExtraInput
1: [ OK ] InteractiveTestHelperTest.DetectsExtraInput (3 ms)
1: [----------] 10 tests from InteractiveTestHelperTest (21 ms total)
1:
1: [----------] 34 tests from ReferenceDataTest
1: [ RUN ] ReferenceDataTest.HandlesSimpleData
1: [ OK ] ReferenceDataTest.HandlesSimpleData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesFloatingPointData
1: [ OK ] ReferenceDataTest.HandlesFloatingPointData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesPresenceChecks
1: [ OK ] ReferenceDataTest.HandlesPresenceChecks (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringBlockData
1: [ OK ] ReferenceDataTest.HandlesStringBlockData (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesVectorData
1: [ OK ] ReferenceDataTest.HandlesVectorData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceData
1: [ OK ] ReferenceDataTest.HandlesSequenceData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceOfCustomData
1: [ OK ] ReferenceDataTest.HandlesSequenceOfCustomData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectData
1: [ OK ] ReferenceDataTest.HandlesIncorrectData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesIncorrectDataType
1: [ OK ] ReferenceDataTest.HandlesIncorrectDataType (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingData
1: [ OK ] ReferenceDataTest.HandlesMissingData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedData
1: [ OK ] ReferenceDataTest.HandlesUncheckedData (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInSequence
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInSequence (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUncheckedDataInCompound
1: [ OK ] ReferenceDataTest.HandlesUncheckedDataInCompound (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnys
1: [ OK ] ReferenceDataTest.HandlesAnys (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTree
1: [ OK ] ReferenceDataTest.HandlesKeyValueTree (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeExtraKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeExtraKey (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesKeyValueTreeMissingKey
1: [ OK ] ReferenceDataTest.HandlesKeyValueTreeMissingKey (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectValue
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectValue (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesAnysWithIncorrectType
1: [ OK ] ReferenceDataTest.HandlesAnysWithIncorrectType (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMissingReferenceDataFile
1: [ OK ] ReferenceDataTest.HandlesMissingReferenceDataFile (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesSpecialCharactersInStrings
1: [ OK ] ReferenceDataTest.HandlesSpecialCharactersInStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace
1: [ OK ] ReferenceDataTest.HandlesStringsWithTextAndWhitespace (30 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmptyStrings
1: [ OK ] ReferenceDataTest.HandlesEmptyStrings (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock
1: [ OK ] ReferenceDataTest.HandlesEmbeddedCdataEndTagInTextBlock (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesSequenceItemIndices
1: [ OK ] ReferenceDataTest.HandlesSequenceItemIndices (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData
1: [ OK ] ReferenceDataTest.HandlesMultipleChecksAgainstSameData (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleNullIds (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds
1: [ OK ] ReferenceDataTest.HandlesMultipleComparisonsAgainstNullIds (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesReadingValues
1: [ OK ] ReferenceDataTest.HandlesReadingValues (0 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithoutChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithValueChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithTypeChanges (1 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithCompoundChanges (2 ms)
1: [ RUN ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries
1: [ OK ] ReferenceDataTest.HandlesUpdateChangedWithRemovedEntries (1 ms)
1: [----------] 34 tests from ReferenceDataTest (72 ms total)
1:
1: [----------] 7 tests from FloatingPointDifferenceTest
1: [ RUN ] FloatingPointDifferenceTest.HandlesEqualValues
1: [ OK ] FloatingPointDifferenceTest.HandlesEqualValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesFloatValues
1: [ OK ] FloatingPointDifferenceTest.HandlesFloatValues (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign
1: [ OK ] FloatingPointDifferenceTest.HandlesZerosOfDifferentSign (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero
1: [ OK ] FloatingPointDifferenceTest.HandlesSignComparisonWithZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferences
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferences (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero
1: [ OK ] FloatingPointDifferenceTest.HandlesUlpDifferenceAcrossZero (0 ms)
1: [ RUN ] FloatingPointDifferenceTest.HandlesNaN
1: [ OK ] FloatingPointDifferenceTest.HandlesNaN (0 ms)
1: [----------] 7 tests from FloatingPointDifferenceTest (1 ms total)
1:
1: [----------] 4 tests from FloatingPointToleranceTest
1: [ RUN ] FloatingPointToleranceTest.UlpTolerance
1: [ OK ] FloatingPointToleranceTest.UlpTolerance (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsFloatingPoint (0 ms)
1: [ RUN ] FloatingPointToleranceTest.RelativeToleranceAsUlp
1: [ OK ] FloatingPointToleranceTest.RelativeToleranceAsUlp (0 ms)
1: [ RUN ] FloatingPointToleranceTest.DefaultFloatTolerance
1: [ OK ] FloatingPointToleranceTest.DefaultFloatTolerance (0 ms)
1: [----------] 4 tests from FloatingPointToleranceTest (0 ms total)
1:
1: [----------] 4 tests from XvgTests
1: [ RUN ] XvgTests.CreateFile
1: [ OK ] XvgTests.CreateFile (2 ms)
1: [ RUN ] XvgTests.CheckMissing
1: [ OK ] XvgTests.CheckMissing (2 ms)
1: [ RUN ] XvgTests.CheckExtra
1: [ OK ] XvgTests.CheckExtra (2 ms)
1: [ RUN ] XvgTests.ReadIncorrect
1: [ OK ] XvgTests.ReadIncorrect (3 ms)
1: [----------] 4 tests from XvgTests (9 ms total)
1:
1: [----------] Global test environment tear-down
1: [==========] 59 tests from 5 test cases ran. (104 ms total)
1: [ PASSED ] 59 tests.
1/54 Test #1: TestUtilsUnitTests .................. Passed 1.67 sec
test 2
Start 2: TestUtilsMpiUnitTests
2: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/testutils-mpi-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TestUtilsMpiUnitTests.xml"
2: Test timeout computed to be: 30
2: [==========] Running 1 test from 1 test case.
2: [----------] Global test environment set-up.
2: [----------] 1 test from MpiSelfTest
2: [ RUN ] MpiSelfTest.Runs
2: [ OK ] MpiSelfTest.Runs (17 ms)
2: [----------] 1 test from MpiSelfTest (17 ms total)
2:
2: [----------] Global test environment tear-down
2: [==========] 1 test from 1 test case ran. (17 ms total)
2: [ PASSED ] 1 test.
2/54 Test #2: TestUtilsMpiUnitTests ............... Passed 0.08 sec
test 3
Start 3: UtilityUnitTests
3: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityUnitTests.xml"
3: Test timeout computed to be: 30
3: [==========] Running 347 tests from 56 test cases.
3: [----------] Global test environment set-up.
3: [----------] 5 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/0.Move
3: [ OK ] AllocatorTest/0.Move (0 ms)
3: [ RUN ] AllocatorTest/0.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/0.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/0 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<double, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/1.Move
3: [ OK ] AllocatorTest/1.Move (0 ms)
3: [ RUN ] AllocatorTest/1.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/1.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/1 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (1 ms)
3: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/2.Move
3: [ OK ] AllocatorTest/2.Move (0 ms)
3: [ RUN ] AllocatorTest/2.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/2.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/2 (1 ms total)
3:
3: [----------] 5 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<int, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/3.Move
3: [ OK ] AllocatorTest/3.Move (0 ms)
3: [ RUN ] AllocatorTest/3.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/3.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/3 (0 ms total)
3:
3: [----------] 5 tests from AllocatorTest/4, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/4.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndResizesWithAlignment (2 ms)
3: [ RUN ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/4.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/4.Move
3: [ OK ] AllocatorTest/4.Move (0 ms)
3: [ RUN ] AllocatorTest/4.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/4.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/4 (2 ms total)
3:
3: [----------] 5 tests from AllocatorTest/5, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::PageAlignedAllocationPolicy>
3: [ RUN ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment
3: [ OK ] AllocatorTest/5.AllocatorAlignAllocatesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndResizesWithAlignment (2 ms)
3: [ RUN ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment
3: [ OK ] AllocatorTest/5.VectorAllocatesAndReservesWithAlignment (0 ms)
3: [ RUN ] AllocatorTest/5.Move
3: [ OK ] AllocatorTest/5.Move (0 ms)
3: [ RUN ] AllocatorTest/5.StatelessAllocatorUsesNoMemory
3: [ OK ] AllocatorTest/5.StatelessAllocatorUsesNoMemory (0 ms)
3: [----------] 5 tests from AllocatorTest/5 (2 ms total)
3:
3: [----------] 1 test from AllocatorUntypedTest
3: [ RUN ] AllocatorUntypedTest.Comparison
3: [ OK ] AllocatorUntypedTest.Comparison (0 ms)
3: [----------] 1 test from AllocatorUntypedTest (0 ms total)
3:
3: [----------] 1 test from EmptyArrayRefTest
3: [ RUN ] EmptyArrayRefTest.IsEmpty
3: [ OK ] EmptyArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyArrayRefTest (0 ms total)
3:
3: [----------] 1 test from EmptyConstArrayRefTest
3: [ RUN ] EmptyConstArrayRefTest.IsEmpty
3: [ OK ] EmptyConstArrayRefTest.IsEmpty (0 ms)
3: [----------] 1 test from EmptyConstArrayRefTest (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/0, where TypeParam = gmx::ArrayRef<char>
3: [ RUN ] ArrayRefTest/0.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/0.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/0.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/0 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/1, where TypeParam = gmx::ArrayRef<unsigned char>
3: [ RUN ] ArrayRefTest/1.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/1.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/1.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/1 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/2, where TypeParam = gmx::ArrayRef<int>
3: [ RUN ] ArrayRefTest/2.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/2.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/2.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/2 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/3, where TypeParam = gmx::ArrayRef<unsigned int>
3: [ RUN ] ArrayRefTest/3.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/3.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/3.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/3 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/4, where TypeParam = gmx::ArrayRef<long>
3: [ RUN ] ArrayRefTest/4.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/4.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/4.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/4 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/5, where TypeParam = gmx::ArrayRef<unsigned long>
3: [ RUN ] ArrayRefTest/5.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/5.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/5.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/5 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/6, where TypeParam = gmx::ArrayRef<long long>
3: [ RUN ] ArrayRefTest/6.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/6.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/6.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/6 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/7, where TypeParam = gmx::ArrayRef<unsigned long long>
3: [ RUN ] ArrayRefTest/7.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/7.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/7.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/7 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/8, where TypeParam = gmx::ArrayRef<float>
3: [ RUN ] ArrayRefTest/8.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/8.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/8.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/8 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/9, where TypeParam = gmx::ArrayRef<double>
3: [ RUN ] ArrayRefTest/9.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/9.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/9.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/9 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/10, where TypeParam = gmx::ArrayRef<char const>
3: [ RUN ] ArrayRefTest/10.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/10.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/10.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/10 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/11, where TypeParam = gmx::ArrayRef<unsigned char const>
3: [ RUN ] ArrayRefTest/11.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/11.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/11.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/11 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/12, where TypeParam = gmx::ArrayRef<int const>
3: [ RUN ] ArrayRefTest/12.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/12.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/12.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/12 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/13, where TypeParam = gmx::ArrayRef<unsigned int const>
3: [ RUN ] ArrayRefTest/13.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/13.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/13.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/13 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/14, where TypeParam = gmx::ArrayRef<long const>
3: [ RUN ] ArrayRefTest/14.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/14.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/14.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/14 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/15, where TypeParam = gmx::ArrayRef<unsigned long const>
3: [ RUN ] ArrayRefTest/15.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/15.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/15.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/15 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/16, where TypeParam = gmx::ArrayRef<long long const>
3: [ RUN ] ArrayRefTest/16.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/16.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/16.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/16 (1 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/17, where TypeParam = gmx::ArrayRef<unsigned long long const>
3: [ RUN ] ArrayRefTest/17.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/17.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/17.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/17 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/18, where TypeParam = gmx::ArrayRef<float const>
3: [ RUN ] ArrayRefTest/18.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/18.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/18.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/18 (0 ms total)
3:
3: [----------] 9 tests from ArrayRefTest/19, where TypeParam = gmx::ArrayRef<double const>
3: [ RUN ] ArrayRefTest/19.MakeWithAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithAssignmentWorks (1 ms)
3: [ RUN ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks
3: [ OK ] ArrayRefTest/19.MakeWithNonConstAssignmentWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructWithNonConstTemplateConstructorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstPointersWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstPointersWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromNonConstVectorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromNonConstVectorWorks (0 ms)
3: [ RUN ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks
3: [ OK ] ArrayRefTest/19.ConstructFromStructFieldWithTemplateConstructorWorks (0 ms)
3: [----------] 9 tests from ArrayRefTest/19 (1 ms total)
3:
3: [----------] 2 tests from CStringUtilityTest
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparison
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparison (0 ms)
3: [ RUN ] CStringUtilityTest.CaseInsensitiveComparisonInLength
3: [ OK ] CStringUtilityTest.CaseInsensitiveComparisonInLength (0 ms)
3: [----------] 2 tests from CStringUtilityTest (0 ms total)
3:
3: [----------] 2 tests from DefaultInitializationAllocator
3: [ RUN ] DefaultInitializationAllocator.PerformsValueInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsValueInitialization (0 ms)
3: [ RUN ] DefaultInitializationAllocator.PerformsNoInitialization
3: [ OK ] DefaultInitializationAllocator.PerformsNoInitialization (0 ms)
3: [----------] 2 tests from DefaultInitializationAllocator (0 ms total)
3:
3: [----------] 4 tests from EnumerationHelpersTest
3: [ RUN ] EnumerationHelpersTest.EnumerationWrapperWorks
3: [ OK ] EnumerationHelpersTest.EnumerationWrapperWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.EnumerationArrayWorks (0 ms)
3: [ RUN ] EnumerationHelpersTest.EnumerationArrayCountIsSafe
3: [ OK ] EnumerationHelpersTest.EnumerationArrayCountIsSafe (0 ms)
3: [ RUN ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks
3: [ OK ] EnumerationHelpersTest.ArrayRefOfEnumerationArrayWorks (0 ms)
3: [----------] 4 tests from EnumerationHelpersTest (0 ms total)
3:
3: [----------] 9 tests from FixedCapacityVectorTest
3: [ RUN ] FixedCapacityVectorTest.IsEmpty
3: [ OK ] FixedCapacityVectorTest.IsEmpty (1 ms)
3: [ RUN ] FixedCapacityVectorTest.PushWorks
3: [ OK ] FixedCapacityVectorTest.PushWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.PopWorks
3: [ OK ] FixedCapacityVectorTest.PopWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ClearWorks
3: [ OK ] FixedCapacityVectorTest.ClearWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.EmplaceBackWorks
3: [ OK ] FixedCapacityVectorTest.EmplaceBackWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.AtThrows
3: [ OK ] FixedCapacityVectorTest.AtThrows (0 ms)
3: [ RUN ] FixedCapacityVectorTest.IteratorWorks
3: [ OK ] FixedCapacityVectorTest.IteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ReverseIteratorWorks
3: [ OK ] FixedCapacityVectorTest.ReverseIteratorWorks (0 ms)
3: [ RUN ] FixedCapacityVectorTest.ZeroCapacityWorks
3: [ OK ] FixedCapacityVectorTest.ZeroCapacityWorks (0 ms)
3: [----------] 9 tests from FixedCapacityVectorTest (1 ms total)
3:
3: [----------] 5 tests from InMemorySerializerTest
3: [ RUN ] InMemorySerializerTest.Roundtrip
3: [ OK ] InMemorySerializerTest.Roundtrip (0 ms)
3: [ RUN ] InMemorySerializerTest.RoundtripWithEndianessSwap
3: [ OK ] InMemorySerializerTest.RoundtripWithEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SerializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.SerializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.DeserializerExplicitEndianessSwap
3: [ OK ] InMemorySerializerTest.DeserializerExplicitEndianessSwap (0 ms)
3: [ RUN ] InMemorySerializerTest.SizeIsCorrect
3: [ OK ] InMemorySerializerTest.SizeIsCorrect (0 ms)
3: [----------] 5 tests from InMemorySerializerTest (1 ms total)
3:
3: [----------] 4 tests from KeyValueTreeSerializerTest
3: [ RUN ] KeyValueTreeSerializerTest.EmptyTree
3: [ OK ] KeyValueTreeSerializerTest.EmptyTree (0 ms)
3: [ RUN ] KeyValueTreeSerializerTest.SimpleObject
3: [ OK ] KeyValueTreeSerializerTest.SimpleObject (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithArrays
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithArrays (1 ms)
3: [ RUN ] KeyValueTreeSerializerTest.ObjectWithObjects
3: [ OK ] KeyValueTreeSerializerTest.ObjectWithObjects (1 ms)
3: [----------] 4 tests from KeyValueTreeSerializerTest (3 ms total)
3:
3: [----------] 6 tests from TreeValueTransformTest
3: [ RUN ] TreeValueTransformTest.SimpleTransforms
3: [ OK ] TreeValueTransformTest.SimpleTransforms (0 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive
3: [ OK ] TreeValueTransformTest.SimpleTransformsCaseAndDashInsensitive (1 ms)
3: [ RUN ] TreeValueTransformTest.SimpleTransformsToObject
3: [ OK ] TreeValueTransformTest.SimpleTransformsToObject (1 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromString
3: [ OK ] TreeValueTransformTest.ObjectFromString (0 ms)
3: [ RUN ] TreeValueTransformTest.ObjectFromMultipleStrings
3: [ OK ] TreeValueTransformTest.ObjectFromMultipleStrings (1 ms)
3: [ RUN ] TreeValueTransformTest.ScopedTransformRules
3: [ OK ] TreeValueTransformTest.ScopedTransformRules (0 ms)
3: [----------] 6 tests from TreeValueTransformTest (3 ms total)
3:
3: [----------] 1 test from TreeValueTransformErrorTest
3: [ RUN ] TreeValueTransformErrorTest.ConversionError
3: [ OK ] TreeValueTransformErrorTest.ConversionError (1 ms)
3: [----------] 1 test from TreeValueTransformErrorTest (1 ms total)
3:
3: [----------] 7 tests from LoggerTest
3: [ RUN ] LoggerTest.EmptyLoggerWorks
3: [ OK ] LoggerTest.EmptyLoggerWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToStream
3: [ OK ] LoggerTest.LogsToStream (1 ms)
3: [ RUN ] LoggerTest.LogsToFile
3: [ OK ] LoggerTest.LogsToFile (1 ms)
3: [ RUN ] LoggerTest.LevelFilteringWorks
3: [ OK ] LoggerTest.LevelFilteringWorks (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleStreams
3: [ OK ] LoggerTest.LogsToMultipleStreams (0 ms)
3: [ RUN ] LoggerTest.LogsToMultipleFiles
3: [ OK ] LoggerTest.LogsToMultipleFiles (4 ms)
3: [ RUN ] LoggerTest.LogsToStreamAndFile
3: [ OK ] LoggerTest.LogsToStreamAndFile (1 ms)
3: [----------] 7 tests from LoggerTest (8 ms total)
3:
3: [----------] 4 tests from MutexBasicTest
3: [ RUN ] MutexBasicTest.CanBeMade
3: [ OK ] MutexBasicTest.CanBeMade (0 ms)
3: [ RUN ] MutexBasicTest.CanBeLocked
3: [ OK ] MutexBasicTest.CanBeLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeTryLocked
3: [ OK ] MutexBasicTest.CanBeTryLocked (0 ms)
3: [ RUN ] MutexBasicTest.CanBeUsedInLockGuard
3: [ OK ] MutexBasicTest.CanBeUsedInLockGuard (0 ms)
3: [----------] 4 tests from MutexBasicTest (0 ms total)
3:
3: [----------] 3 tests from MutexTaskTest
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithLock
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithLock (3 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnOtherThread (0 ms)
3: [ RUN ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread
3: [ OK ] MutexTaskTest.MutualExclusionWorksWithTryLockOnSameThread (0 ms)
3: [----------] 3 tests from MutexTaskTest (4 ms total)
3:
3: [----------] 2 tests from PathTest
3: [ RUN ] PathTest.StripSourcePrefixWorks
3: [ OK ] PathTest.StripSourcePrefixWorks (0 ms)
3: [ RUN ] PathTest.SearchOperationsWork
3: [ OK ] PathTest.SearchOperationsWork (1 ms)
3: [----------] 2 tests from PathTest (2 ms total)
3:
3: [----------] 2 tests from PhysicalNodeCommunicatorTest
3: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
3: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (0 ms)
3: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
3: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (0 ms)
3: [----------] 2 tests from PhysicalNodeCommunicatorTest (0 ms total)
3:
3: [----------] 9 tests from StringUtilityTest
3: [ RUN ] StringUtilityTest.StartsWith
3: [ OK ] StringUtilityTest.StartsWith (0 ms)
3: [ RUN ] StringUtilityTest.EndsWith
3: [ OK ] StringUtilityTest.EndsWith (0 ms)
3: [ RUN ] StringUtilityTest.StripSuffixIfPresent
3: [ OK ] StringUtilityTest.StripSuffixIfPresent (0 ms)
3: [ RUN ] StringUtilityTest.StripString
3: [ OK ] StringUtilityTest.StripString (0 ms)
3: [ RUN ] StringUtilityTest.SplitString
3: [ OK ] StringUtilityTest.SplitString (1 ms)
3: [ RUN ] StringUtilityTest.SplitDelimitedString
3: [ OK ] StringUtilityTest.SplitDelimitedString (0 ms)
3: [ RUN ] StringUtilityTest.SplitAndTrimDelimitedString
3: [ OK ] StringUtilityTest.SplitAndTrimDelimitedString (1 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitive
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitive (0 ms)
3: [ RUN ] StringUtilityTest.CanCompareCaseInsensitiveInLength
3: [ OK ] StringUtilityTest.CanCompareCaseInsensitiveInLength (0 ms)
3: [----------] 9 tests from StringUtilityTest (2 ms total)
3:
3: [----------] 2 tests from FormatStringTest
3: [ RUN ] FormatStringTest.HandlesBasicFormatting
3: [ OK ] FormatStringTest.HandlesBasicFormatting (0 ms)
3: [ RUN ] FormatStringTest.HandlesLongStrings
3: [ OK ] FormatStringTest.HandlesLongStrings (0 ms)
3: [----------] 2 tests from FormatStringTest (0 ms total)
3:
3: [----------] 1 test from StringFormatterTest
3: [ RUN ] StringFormatterTest.HandlesBasicFormatting
3: [ OK ] StringFormatterTest.HandlesBasicFormatting (0 ms)
3: [----------] 1 test from StringFormatterTest (0 ms total)
3:
3: [----------] 1 test from formatAndJoinTest
3: [ RUN ] formatAndJoinTest.Works
3: [ OK ] formatAndJoinTest.Works (0 ms)
3: [----------] 1 test from formatAndJoinTest (0 ms total)
3:
3: [----------] 1 test from JoinStringsTest
3: [ RUN ] JoinStringsTest.Works
3: [ OK ] JoinStringsTest.Works (0 ms)
3: [----------] 1 test from JoinStringsTest (0 ms total)
3:
3: [----------] 6 tests from ReplaceAllTest
3: [ RUN ] ReplaceAllTest.HandlesEmptyStrings
3: [ OK ] ReplaceAllTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesNoMatches
3: [ OK ] ReplaceAllTest.HandlesNoMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMatchesAtEnds
3: [ OK ] ReplaceAllTest.HandlesMatchesAtEnds (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesMultipleMatches
3: [ OK ] ReplaceAllTest.HandlesMultipleMatches (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesWordBoundaries
3: [ OK ] ReplaceAllTest.HandlesWordBoundaries (0 ms)
3: [ RUN ] ReplaceAllTest.HandlesPossibleRecursiveMatches
3: [ OK ] ReplaceAllTest.HandlesPossibleRecursiveMatches (1 ms)
3: [----------] 6 tests from ReplaceAllTest (1 ms total)
3:
3: [----------] 10 tests from TextLineWrapperTest
3: [ RUN ] TextLineWrapperTest.HandlesEmptyStrings
3: [ OK ] TextLineWrapperTest.HandlesEmptyStrings (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingWhitespace
3: [ OK ] TextLineWrapperTest.HandlesTrailingWhitespace (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesTrailingNewlines
3: [ OK ] TextLineWrapperTest.HandlesTrailingNewlines (0 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectly
3: [ OK ] TextLineWrapperTest.WrapsCorrectly (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExistingBreaks (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndent
3: [ OK ] TextLineWrapperTest.HandlesIndent (1 ms)
3: [ RUN ] TextLineWrapperTest.HandlesIndentWithEmptyLines
3: [ OK ] TextLineWrapperTest.HandlesIndentWithEmptyLines (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesHangingIndent
3: [ OK ] TextLineWrapperTest.HandlesHangingIndent (0 ms)
3: [ RUN ] TextLineWrapperTest.HandlesContinuationCharacter
3: [ OK ] TextLineWrapperTest.HandlesContinuationCharacter (1 ms)
3: [ RUN ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace
3: [ OK ] TextLineWrapperTest.WrapsCorrectlyWithExtraWhitespace (0 ms)
3: [----------] 10 tests from TextLineWrapperTest (3 ms total)
3:
3: [----------] 6 tests from TextWriterTest
3: [ RUN ] TextWriterTest.WritesLines
3: [ OK ] TextWriterTest.WritesLines (1 ms)
3: [ RUN ] TextWriterTest.WritesLinesInParts
3: [ OK ] TextWriterTest.WritesLinesInParts (0 ms)
3: [ RUN ] TextWriterTest.WritesWrappedLines
3: [ OK ] TextWriterTest.WritesWrappedLines (0 ms)
3: [ RUN ] TextWriterTest.WritesLinesInPartsWithWrapper
3: [ OK ] TextWriterTest.WritesLinesInPartsWithWrapper (1 ms)
3: [ RUN ] TextWriterTest.TracksNewlines
3: [ OK ] TextWriterTest.TracksNewlines (0 ms)
3: [ RUN ] TextWriterTest.PreservesTrailingWhitespace
3: [ OK ] TextWriterTest.PreservesTrailingWhitespace (0 ms)
3: [----------] 6 tests from TextWriterTest (3 ms total)
3:
3: [----------] 1 test from TypeTraitsTest
3: [ RUN ] TypeTraitsTest.IsIntegralConstant
3: [ OK ] TypeTraitsTest.IsIntegralConstant (0 ms)
3: [----------] 1 test from TypeTraitsTest (0 ms total)
3:
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitBit/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Disjoint/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.Union/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.Union/0 (0 ms)
3: [ RUN ] BitmaskTest32_11/BitmaskTest32.ToHex/0
3: [ OK ] BitmaskTest32_11/BitmaskTest32.ToHex/0 (0 ms)
3: [----------] 6 tests from BitmaskTest32_11/BitmaskTest32 (0 ms total)
3:
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.Union/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.Union/1 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1
3: [ OK ] BitmaskTest64_10_42/BitmaskTest64.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest64_10_42/BitmaskTest64 (1 ms total)
3:
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.SetAndClear/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitBit/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.InitLowBits/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Disjoint/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.Union/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.Union/1 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/0 (0 ms)
3: [ RUN ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1
3: [ OK ] BitmaskTest128_9_78/BitmaskTest128.ToHex/1 (0 ms)
3: [----------] 12 tests from BitmaskTest128_9_78/BitmaskTest128 (0 ms total)
3:
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/0 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDefaultPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/0 (1 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithAsyncLaunchPolicy/2 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/0 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/1 (0 ms)
3: [ RUN ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2
3: [ OK ] WithAndWithoutMutex/DifferentTasksTest.StdAsyncWorksWithDeferredLaunchPolicy/2 (0 ms)
3: [----------] 9 tests from WithAndWithoutMutex/DifferentTasksTest (2 ms total)
3:
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/0 (1 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/1 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/2 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/3 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/4 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/5 (0 ms)
3: [ RUN ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6
3: [ OK ] ParsesLinesDifferently/TextReaderTest.UsingDifferentConfigurations/6 (0 ms)
3: [----------] 7 tests from ParsesLinesDifferently/TextReaderTest (3 ms total)
3:
3: [----------] Global test environment tear-down
3: [==========] 347 tests from 56 test cases ran. (58 ms total)
3: [ PASSED ] 347 tests.
3/54 Test #3: UtilityUnitTests .................... Passed 0.18 sec
test 4
Start 4: UtilityMpiUnitTests
4: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/utility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/UtilityMpiUnitTests.xml"
4: Test timeout computed to be: 30
4: [==========] Running 2 tests from 1 test case.
4: [----------] Global test environment set-up.
4: [----------] 2 tests from PhysicalNodeCommunicatorTest
4: [ RUN ] PhysicalNodeCommunicatorTest.CanConstruct
4: [ OK ] PhysicalNodeCommunicatorTest.CanConstruct (2 ms)
4: [ RUN ] PhysicalNodeCommunicatorTest.CanCallBarrier
4: [ OK ] PhysicalNodeCommunicatorTest.CanCallBarrier (15 ms)
4: [----------] 2 tests from PhysicalNodeCommunicatorTest (18 ms total)
4:
4: [----------] Global test environment tear-down
4: [==========] 2 tests from 1 test case ran. (19 ms total)
4: [ PASSED ] 2 tests.
4/54 Test #4: UtilityMpiUnitTests ................. Passed 0.08 sec
test 5
Start 5: MdlibUnitTest
5: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdlib-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdlibUnitTest.xml"
5: Test timeout computed to be: 30
5: [==========] Running 187 tests from 13 test cases.
5: [----------] Global test environment set-up.
5: [----------] 1 test from VerletBufferConstraintTest
5: [ RUN ] VerletBufferConstraintTest.EqualMasses
5: [ OK ] VerletBufferConstraintTest.EqualMasses (1 ms)
5: [----------] 1 test from VerletBufferConstraintTest (1 ms total)
5:
5: [----------] 2 tests from PrEbinTest
5: [ RUN ] PrEbinTest.HandlesAverages
5: [ OK ] PrEbinTest.HandlesAverages (2 ms)
5: [ RUN ] PrEbinTest.HandlesEmptyAverages
5: [ OK ] PrEbinTest.HandlesEmptyAverages (1 ms)
5: [----------] 2 tests from PrEbinTest (4 ms total)
5:
5: [----------] 4 tests from ShakeTest
5: [ RUN ] ShakeTest.ConstrainsOneBond
5: [ OK ] ShakeTest.ConstrainsOneBond (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoDisjointBonds
5: [ OK ] ShakeTest.ConstrainsTwoDisjointBonds (0 ms)
5: [ RUN ] ShakeTest.ConstrainsTwoBondsWithACommonAtom
5: [ OK ] ShakeTest.ConstrainsTwoBondsWithACommonAtom (0 ms)
5: [ RUN ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms
5: [ OK ] ShakeTest.ConstrainsThreeBondsWithCommonAtoms (0 ms)
5: [----------] 4 tests from ShakeTest (2 ms total)
5:
5: [----------] 1 test from NullSignalTest
5: [ RUN ] NullSignalTest.NullSignallerWorks
5: [ OK ] NullSignalTest.NullSignallerWorks (0 ms)
5: [----------] 1 test from NullSignalTest (0 ms total)
5:
5: [----------] 7 tests from SignalTest
5: [ RUN ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace
5: [ OK ] SignalTest.NoSignalPropagatesIfNoSignallingTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenInterSimTakesPlace (0 ms)
5: [ RUN ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.LocalIntraSimSignalPropagatesWhenBothTakePlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalDoesntPropagateWhenIntraSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenInterSimSignalTakesPlace (0 ms)
5: [ RUN ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace
5: [ OK ] SignalTest.NonLocalSignalPropagatesWhenBothTakePlace (0 ms)
5: [----------] 7 tests from SignalTest (3 ms total)
5:
5: [----------] 9 tests from UpdateGroups
5: [ RUN ] UpdateGroups.ethaneUA
5: [ OK ] UpdateGroups.ethaneUA (1 ms)
5: [ RUN ] UpdateGroups.methane
5: [ OK ] UpdateGroups.methane (0 ms)
5: [ RUN ] UpdateGroups.ethane
5: [ OK ] UpdateGroups.ethane (0 ms)
5: [ RUN ] UpdateGroups.butaneUA
5: [ OK ] UpdateGroups.butaneUA (0 ms)
5: [ RUN ] UpdateGroups.waterThreeSite
5: [ OK ] UpdateGroups.waterThreeSite (0 ms)
5: [ RUN ] UpdateGroups.waterFourSite
5: [ OK ] UpdateGroups.waterFourSite (0 ms)
5: [ RUN ] UpdateGroups.fourAtomsWithSettle
5: [ OK ] UpdateGroups.fourAtomsWithSettle (0 ms)
5: [ RUN ] UpdateGroups.waterFlexAngle
5: [ OK ] UpdateGroups.waterFlexAngle (0 ms)
5: [ RUN ] UpdateGroups.twoMoltypes
5: [ OK ] UpdateGroups.twoMoltypes (0 ms)
5: [----------] 9 tests from UpdateGroups (5 ms total)
5:
5: [----------] 1 test from UpdateGroupsCog
5: [ RUN ] UpdateGroupsCog.ComputesCogs
5: [ OK ] UpdateGroupsCog.ComputesCogs (42 ms)
5: [----------] 1 test from UpdateGroupsCog (43 ms total)
5:
5: [----------] 84 tests from WithParameters/ConstraintsTest
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/0
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/0 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/1
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/1 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/2
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.SingleConstraint/3
5: [ OK ] WithParameters/ConstraintsTest.SingleConstraint/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TwoDisjointConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeSequentialConstraints/11 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15
5: [ OK ] WithParameters/ConstraintsTest.ThreeConstraintsWithCentralAtom/15 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/3 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/6 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/7 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/11 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/15 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/17 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.FourSequentialConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.FourSequentialConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/0
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/0 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/1
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/1 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/2
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/2 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/3
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/3 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/4
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/4 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/5
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/5 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/6
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/6 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/7
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/7 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/8
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/8 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/9
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/9 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/10
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/10 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/11
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/11 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/12
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/12 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/13
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/13 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/14
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/14 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/15
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/15 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/16
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/16 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/17
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/17 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/18
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/18 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/19
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/19 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/20
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/20 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/21
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/21 (0 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/22
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/22 (1 ms)
5: [ RUN ] WithParameters/ConstraintsTest.TriangleOfConstraints/23
5: [ OK ] WithParameters/ConstraintsTest.TriangleOfConstraints/23 (0 ms)
5: [----------] 84 tests from WithParameters/ConstraintsTest (53 ms total)
5:
5: [----------] 11 tests from WithParameters/EnergyOutputTest
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/0
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_0.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/0 (14 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/1
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_1.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/1 (8 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/2
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_2.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/2 (12 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/3
5: [ OK ] WithParameters/EnergyOutputTest.CheckOutput/3 (2 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/4
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_4.edr as double precision energy file
5:
Reading energy frame 0 time 10.100
Reading energy frame 1 time 27.500
Reading energy frame 2 time 44.900
Reading energy frame 3 time 62.300
Reading energy frame 4 time 79.700
Reading energy frame 5 time 97.100
Reading energy frame 6 time 114.500
Reading energy frame 7 time 131.900
Reading energy frame 8 time 149.300
Reading energy frame 9 time 166.700 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/4 (75 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/5
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_5.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/5 (36 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/6
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_6.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/6 (12 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/7
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_7.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/7 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/8
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_8.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/8 (13 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/9
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_9.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/9 (33 ms)
5: [ RUN ] WithParameters/EnergyOutputTest.CheckOutput/10
5: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/mdlib/tests/Testing/Temporary/WithParameters_EnergyOutputTest_CheckOutput_10.edr as double precision energy file
5:
Reading energy frame 0 time 10.100 [ OK ] WithParameters/EnergyOutputTest.CheckOutput/10 (13 ms)
5: [----------] 11 tests from WithParameters/EnergyOutputTest (260 ms total)
5:
5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/1 (1 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.UnknownCalculationModeThrows/7 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.KnownCalculationModeDoesNotThrow/7 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/0 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/1 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/2 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/3 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/4 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/5 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/6 (0 ms)
5: [ RUN ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7
5: [ OK ] SimpleTests/CalculateAcceptanceWeightSimple.BarkerAndMinVarAreIdentical/7 (0 ms)
5: [----------] 24 tests from SimpleTests/CalculateAcceptanceWeightSimple (2 ms total)
5:
5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/0 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/1 (1 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/2 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/3 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/4 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/5 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/6 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/7 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/8 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/9 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/10 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/11 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/12 (0 ms)
5: [ RUN ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13
5: [ OK ] RegressionTests/CalculateAcceptanceWeightRangeRegression.ValuesMatch/13 (0 ms)
5: [----------] 14 tests from RegressionTests/CalculateAcceptanceWeightRangeRegression (1 ms total)
5:
5: [----------] 16 tests from WithParameters/LeapFrogTest
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/0
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/0 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/1
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/1 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/2
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/2 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/3
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/3 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/4
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/4 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/5
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/5 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/6
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/6 (57 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/7
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/7 (1 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/8
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/8 (0 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/9
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/9 (2 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/10
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/10 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/11
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/11 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/12
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/12 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/13
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/13 (11 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/14
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/14 (21 ms)
5: [ RUN ] WithParameters/LeapFrogTest.SimpleIntegration/15
5: [ OK ] WithParameters/LeapFrogTest.SimpleIntegration/15 (11 ms)
5: [----------] 16 tests from WithParameters/LeapFrogTest (172 ms total)
5:
5: [----------] 13 tests from WithParameters/SettleTest
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/0
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/0 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/1
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/1 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/2
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/2 (1 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/3
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/3 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/4
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/4 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/5
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/5 (2 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/6
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/6 (3 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/7
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/7 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/8
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/8 (7 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/9
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/9 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/10
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/10 (4 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/11
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/11 (7 ms)
5: [ RUN ] WithParameters/SettleTest.SatisfiesConstraints/12
5: [ OK ] WithParameters/SettleTest.SatisfiesConstraints/12 (8 ms)
5: [----------] 13 tests from WithParameters/SettleTest (53 ms total)
5:
5: [----------] Global test environment tear-down
5: [==========] 187 tests from 13 test cases ran. (604 ms total)
5: [ PASSED ] 187 tests.
5/54 Test #5: MdlibUnitTest ....................... Passed 0.70 sec
test 6
Start 6: AppliedForcesUnitTest
6: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/applied_forces-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AppliedForcesUnitTest.xml"
6: Test timeout computed to be: 30
6: [==========] Running 20 tests from 4 test cases.
6: [----------] Global test environment set-up.
6: [----------] 2 tests from DensityFittingTest
6: [ RUN ] DensityFittingTest.ForceProviderLackingInputThrows
6: [ OK ] DensityFittingTest.ForceProviderLackingInputThrows (2 ms)
6: [ RUN ] DensityFittingTest.SingleAtom
6: [ OK ] DensityFittingTest.SingleAtom (2 ms)
6: [----------] 2 tests from DensityFittingTest (5 ms total)
6:
6: [----------] 8 tests from DensityFittingOptionsTest
6: [ RUN ] DensityFittingOptionsTest.DefaultParameters
6: [ OK ] DensityFittingOptionsTest.DefaultParameters (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OptionSetsActive
6: [ OK ] DensityFittingOptionsTest.OptionSetsActive (1 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive
6: [ OK ] DensityFittingOptionsTest.OutputNoDefaultValuesWhenInactive (0 ms)
6: [ RUN ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive
6: [ OK ] DensityFittingOptionsTest.OutputDefaultValuesWhenActive (2 ms)
6: [ RUN ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup
6: [ OK ] DensityFittingOptionsTest.CanConvertGroupStringToIndexGroup (1 ms)
6: [ RUN ] DensityFittingOptionsTest.InternalsToKvt
6: [ OK ] DensityFittingOptionsTest.InternalsToKvt (0 ms)
6: [ RUN ] DensityFittingOptionsTest.KvtToInternal
6: [ OK ] DensityFittingOptionsTest.KvtToInternal (1 ms)
6: [ RUN ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent
6: [ OK ] DensityFittingOptionsTest.RoundTripForInternalsIsIdempotent (1 ms)
6: [----------] 8 tests from DensityFittingOptionsTest (6 ms total)
6:
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest
6: [ RUN ] DensityFittingAmplitudeLookupTest.Unity
6: [ OK ] DensityFittingAmplitudeLookupTest.Unity (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Charge
6: [ OK ] DensityFittingAmplitudeLookupTest.Charge (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.Masses
6: [ OK ] DensityFittingAmplitudeLookupTest.Masses (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanCopyConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanCopyConstruct (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveAssign
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveAssign (0 ms)
6: [ RUN ] DensityFittingAmplitudeLookupTest.CanMoveConstruct
6: [ OK ] DensityFittingAmplitudeLookupTest.CanMoveConstruct (0 ms)
6: [----------] 7 tests from DensityFittingAmplitudeLookupTest (1 ms total)
6:
6: [----------] 3 tests from ElectricFieldTest
6: [ RUN ] ElectricFieldTest.Static
6: [ OK ] ElectricFieldTest.Static (0 ms)
6: [ RUN ] ElectricFieldTest.Oscillating
6: [ OK ] ElectricFieldTest.Oscillating (0 ms)
6: [ RUN ] ElectricFieldTest.Pulsed
6: [ OK ] ElectricFieldTest.Pulsed (1 ms)
6: [----------] 3 tests from ElectricFieldTest (2 ms total)
6:
6: [----------] Global test environment tear-down
6: [==========] 20 tests from 4 test cases ran. (18 ms total)
6: [ PASSED ] 20 tests.
6/54 Test #6: AppliedForcesUnitTest ............... Passed 0.08 sec
test 7
Start 7: CommandLineUnitTests
7: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/commandline-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CommandLineUnitTests.xml"
7: Test timeout computed to be: 30
7: [==========] Running 59 tests from 7 test cases.
7: [----------] Global test environment set-up.
7: [----------] 3 tests from CommandLineHelpModuleTest
7: [ RUN ] CommandLineHelpModuleTest.PrintsGeneralHelp
7: [ OK ] CommandLineHelpModuleTest.PrintsGeneralHelp (5 ms)
7: [ RUN ] CommandLineHelpModuleTest.PrintsHelpOnTopic
7: [ OK ] CommandLineHelpModuleTest.PrintsHelpOnTopic (2 ms)
7: [ RUN ] CommandLineHelpModuleTest.ExportsHelp
7: [ OK ] CommandLineHelpModuleTest.ExportsHelp (6 ms)
7: [----------] 3 tests from CommandLineHelpModuleTest (13 ms total)
7:
7: [----------] 7 tests from CommandLineHelpWriterTest
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionTypes
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionTypes (3 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables
7: [ OK ] CommandLineHelpWriterTest.HandlesDefaultValuesFromVariables (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongFileOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongFileOptions (2 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesLongOptions
7: [ OK ] CommandLineHelpWriterTest.HandlesLongOptions (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesOptionGroups
7: [ OK ] CommandLineHelpWriterTest.HandlesOptionGroups (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesHelpText
7: [ OK ] CommandLineHelpWriterTest.HandlesHelpText (1 ms)
7: [ RUN ] CommandLineHelpWriterTest.HandlesKnownIssues
7: [ OK ] CommandLineHelpWriterTest.HandlesKnownIssues (1 ms)
7: [----------] 7 tests from CommandLineHelpWriterTest (10 ms total)
7:
7: [----------] 6 tests from CommandLineModuleManagerTest
7: [ RUN ] CommandLineModuleManagerTest.RunsModule
7: [ OK ] CommandLineModuleManagerTest.RunsModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelp
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelp (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpAfterQuiet (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashH (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule
7: [ OK ] CommandLineModuleManagerTest.RunsModuleHelpWithDashHWithSingleModule (1 ms)
7: [ RUN ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames
7: [ OK ] CommandLineModuleManagerTest.HandlesConflictingBinaryAndModuleNames (0 ms)
7: [----------] 6 tests from CommandLineModuleManagerTest (5 ms total)
7:
7: [----------] 13 tests from CommandLineParserTest
7: [ RUN ] CommandLineParserTest.HandlesSingleValues
7: [ OK ] CommandLineParserTest.HandlesSingleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument
7: [ OK ] CommandLineParserTest.HandlesBooleanAsNoWithoutArgument (0 ms)
7: [ RUN ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument
7: [ OK ] CommandLineParserTest.ThrowsWithBooleanAsNoWithArgument (1 ms)
7: [ RUN ] CommandLineParserTest.HandlesNegativeNumbers
7: [ OK ] CommandLineParserTest.HandlesNegativeNumbers (1 ms)
7: [ RUN ] CommandLineParserTest.HandlesString
7: [ OK ] CommandLineParserTest.HandlesString (0 ms)
7: [ RUN ] CommandLineParserTest.RejectsStringWithMultipleValues
7: [ OK ] CommandLineParserTest.RejectsStringWithMultipleValues (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesDoubleDashOptionPrefix
7: [ OK ] CommandLineParserTest.HandlesDoubleDashOptionPrefix (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesOptionsStartingWithNumbers
7: [ OK ] CommandLineParserTest.HandlesOptionsStartingWithNumbers (0 ms)
7: [ RUN ] CommandLineParserTest.HandlesSkipUnknown
7: [ OK ] CommandLineParserTest.HandlesSkipUnknown (1 ms)
7: [ RUN ] CommandLineParserTest.RejectsPositionalArgumentsByDefault
7: [ OK ] CommandLineParserTest.RejectsPositionalArgumentsByDefault (0 ms)
7: [ RUN ] CommandLineParserTest.CanAllowPositionalArguments
7: [ OK ] CommandLineParserTest.CanAllowPositionalArguments (1 ms)
7: [ RUN ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions
7: [ OK ] CommandLineParserTest.CannotHavePositionalArgumentsAfterOptions (0 ms)
7: [----------] 13 tests from CommandLineParserTest (4 ms total)
7:
7: [----------] 6 tests from CommandLineProgramContextTest
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithAbsolutePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryWithRelativePath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryWithRelativePath (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromPath
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromPath (1 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromCurrentDirectory (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromAbsoluteSymLink (0 ms)
7: [ RUN ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink
7: [ OK ] CommandLineProgramContextTest.FindsBinaryFromRelativeSymLink (0 ms)
7: [----------] 6 tests from CommandLineProgramContextTest (1 ms total)
7:
7: [----------] 3 tests from OutputNamesTest
7: [ RUN ] OutputNamesTest.CanBeSuffixed
7: [ OK ] OutputNamesTest.CanBeSuffixed (1 ms)
7: [ RUN ] OutputNamesTest.HasSuffixFromNoAppend
7: [ OK ] OutputNamesTest.HasSuffixFromNoAppend (0 ms)
7: [ RUN ] OutputNamesTest.CanHavePartNumberAdded
7: [ OK ] OutputNamesTest.CanHavePartNumberAdded (0 ms)
7: [----------] 3 tests from OutputNamesTest (1 ms total)
7:
7: [----------] 21 tests from ParseCommonArgsTest
7: [ RUN ] ParseCommonArgsTest.ParsesIntegerArgs
7: [ OK ] ParseCommonArgsTest.ParsesIntegerArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesInt64Args
7: [ OK ] ParseCommonArgsTest.ParsesInt64Args (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesRealArgs
7: [ OK ] ParseCommonArgsTest.ParsesRealArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesStringArgs
7: [ OK ] ParseCommonArgsTest.ParsesStringArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesBooleanArgs
7: [ OK ] ParseCommonArgsTest.ParsesBooleanArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesVectorArgs
7: [ OK ] ParseCommonArgsTest.ParsesVectorArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgs
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit
7: [ OK ] ParseCommonArgsTest.ParsesTimeArgsWithTimeUnit (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesEnumArgs
7: [ OK ] ParseCommonArgsTest.ParsesEnumArgs (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgs
7: [ OK ] ParseCommonArgsTest.ParsesFileArgs (1 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaults
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaults (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.ParsesFileArgsWithDefaultFileName (0 ms)
7: [ RUN ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension
7: [ OK ] ParseCommonArgsTest.ParseFileArgsWithCustomDefaultExtension (1 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentInputFiles (0 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles
7: [ OK ] ParseCommonArgsTest.HandlesNonExistentOptionalInputFiles (1 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified
7: [ OK ] ParseCommonArgsTest.AcceptsNonExistentInputFilesIfSpecified (1 ms)
7: [ RUN ] ParseCommonArgsTest.HandlesCompressedFiles
7: [ OK ] ParseCommonArgsTest.HandlesCompressedFiles (2 ms)
7: [ RUN ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension
7: [ OK ] ParseCommonArgsTest.AcceptsUnknownTrajectoryExtension (1 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFile
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFile (5 ms)
7: [ RUN ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName
7: [ OK ] ParseCommonArgsTest.CompletesExtensionFromExistingFileWithDefaultFileName (3 ms)
7: [ RUN ] ParseCommonArgsTest.CanKeepUnknownArgs
7: [ OK ] ParseCommonArgsTest.CanKeepUnknownArgs (1 ms)
7: [----------] 21 tests from ParseCommonArgsTest (20 ms total)
7:
7: [----------] Global test environment tear-down
7: [==========] 59 tests from 7 test cases ran. (57 ms total)
7: [ PASSED ] 59 tests.
7/54 Test #7: CommandLineUnitTests ................ Passed 0.13 sec
test 8
Start 8: DomDecTests
8: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/domdec-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/DomDecTests.xml"
8: Test timeout computed to be: 30
8: [==========] Running 9 tests from 2 test cases.
8: [----------] Global test environment set-up.
8: [----------] 7 tests from HashedMap
8: [ RUN ] HashedMap.InsertsFinds
8: [ OK ] HashedMap.InsertsFinds (0 ms)
8: [ RUN ] HashedMap.NegativeKeysWork
8: [ OK ] HashedMap.NegativeKeysWork (0 ms)
8: [ RUN ] HashedMap.InsertsErases
8: [ OK ] HashedMap.InsertsErases (0 ms)
8: [ RUN ] HashedMap.InsertsOrAssigns
8: [ OK ] HashedMap.InsertsOrAssigns (0 ms)
8: [ RUN ] HashedMap.Clears
8: [ OK ] HashedMap.Clears (1 ms)
8: [ RUN ] HashedMap.LinkedEntries
8: [ OK ] HashedMap.LinkedEntries (0 ms)
8: [ RUN ] HashedMap.ResizesTable
8: [ OK ] HashedMap.ResizesTable (0 ms)
8: [----------] 7 tests from HashedMap (1 ms total)
8:
8: [----------] 2 tests from LocalAtomSetManager
8: [ RUN ] LocalAtomSetManager.CanAddEmptyLocalAtomSet
8: [ OK ] LocalAtomSetManager.CanAddEmptyLocalAtomSet (0 ms)
8: [ RUN ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices
8: [ OK ] LocalAtomSetManager.CanAddandReadLocalAtomSetIndices (0 ms)
8: [----------] 2 tests from LocalAtomSetManager (0 ms total)
8:
8: [----------] Global test environment tear-down
8: [==========] 9 tests from 2 test cases ran. (1 ms total)
8: [ PASSED ] 9 tests.
8/54 Test #8: DomDecTests ......................... Passed 0.06 sec
test 9
Start 9: EwaldUnitTests
9: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/ewald-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EwaldUnitTests.xml"
9: Test timeout computed to be: 30
9: [==========] Running 257 tests from 10 test cases.
9: [----------] Global test environment set-up.
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/0 (1 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/1 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/2 (0 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/3 (14 ms)
9: [ RUN ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4
9: [ OK ] InsaneInput/PmeBSplineModuliFailureTest.Throws/4 (1 ms)
9: [----------] 5 tests from InsaneInput/PmeBSplineModuliFailureTest (16 ms total)
9:
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/0 (14 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/1 (13 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/2 (13 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/3 (13 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/4 (14 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/5 (14 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/6 (14 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/7 (14 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/8 (16 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/9 (15 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/10 (16 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/11 (16 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/12 (31 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/13 (14 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/14 (15 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/15 (15 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/16 (16 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/17 (16 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/18 (18 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/19 (30 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/20 (21 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/21 (17 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/22 (22 ms)
9: [ RUN ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23
9: [ OK ] SaneInput1/PmeBSplineModuliCorrectnessTest.ReproducesValues/23 (38 ms)
9: [----------] 24 tests from SaneInput1/PmeBSplineModuliCorrectnessTest (446 ms total)
9:
9: [----------] 144 tests from SaneInput/PmeGatherTest
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/0 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/1 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/2 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/3 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/4 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/5 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/6 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/7 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/8 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/9 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/10 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/11 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/12 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/13 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/14 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/15 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/16
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/16 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/17
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/17 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/18
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/18 (6 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/19
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/19 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/20
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/20 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/21
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/21 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/22
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/22 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/23
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/23 (8 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/24
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/24 (5 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/25
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/25 (6 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/26
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/26 (4 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/27
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/27 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/28
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/28 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/29
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/29 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/30
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/30 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/31
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/31 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/32
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/32 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/33
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/33 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/34
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/34 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/35
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/35 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/36
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/36 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/37
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/37 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/38
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/38 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/39
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/39 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/40
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/40 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/41
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/41 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/42
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/42 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/43
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/43 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/44
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/44 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/45
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/45 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/46
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/46 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/47
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/47 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/48
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/48 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/49
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/49 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/50
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/50 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/51
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/51 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/52
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/52 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/53
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/53 (6 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/54
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/54 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/55
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/55 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/56
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/56 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/57
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/57 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/58
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/58 (4 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/59
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/59 (6 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/60
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/60 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/61
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/61 (4 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/62
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/62 (6 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/63
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/63 (4 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/64
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/64 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/65
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/65 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/66
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/66 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/67
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/67 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/68
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/68 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/69
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/69 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/70
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/70 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/71
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/71 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/72
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/72 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/73
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/73 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/74
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/74 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/75
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/75 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/76
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/76 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/77
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/77 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/78
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/78 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/79
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/79 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/80
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/80 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/81
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/81 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/82
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/82 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/83
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/83 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/84
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/84 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/85
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/85 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/86
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/86 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/87
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/87 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/88
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/88 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/89
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/89 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/90
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/90 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/91
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/91 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/92
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/92 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/93
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/93 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/94
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/94 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/95
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/95 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/96
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/96 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/97
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/97 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/98
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/98 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/99
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/99 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/100
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/100 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/101
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/101 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/102
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/102 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/103
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/103 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/104
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/104 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/105
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/105 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/106
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/106 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/107
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/107 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/108
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/108 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/109
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/109 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/110
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/110 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/111
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/111 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/112
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/112 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/113
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/113 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/114
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/114 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/115
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/115 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/116
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/116 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/117
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/117 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/118
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/118 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/119
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/119 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/120
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/120 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/121
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/121 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/122
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/122 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/123
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/123 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/124
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/124 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/125
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/125 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/126
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/126 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/127
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/127 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/128
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/128 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/129
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/129 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/130
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/130 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/131
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/131 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/132
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/132 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/133
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/133 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/134
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/134 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/135
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/135 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/136
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/136 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/137
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/137 (3 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/138
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/138 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/139
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/139 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/140
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/140 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/141
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/141 (2 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/142
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/142 (1 ms)
9: [ RUN ] SaneInput/PmeGatherTest.ReproducesOutputs/143
9: [ OK ] SaneInput/PmeGatherTest.ReproducesOutputs/143 (2 ms)
9: [----------] 144 tests from SaneInput/PmeGatherTest (305 ms total)
9:
9: [----------] 16 tests from SaneInput/PmeSolveTest
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/0 (7 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/1 (11 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/2 (6 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/3 (10 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/4 (9 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/5 (6 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/7 (5 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/8 (5 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/9 (11 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/10 (6 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/11 (11 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/12 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/13 (6 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/14 (4 ms)
9: [ RUN ] SaneInput/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] SaneInput/PmeSolveTest.ReproducesOutputs/15 (6 ms)
9: [----------] 16 tests from SaneInput/PmeSolveTest (113 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/0 (6 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/1 (5 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/2 (4 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/3 (4 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/4 (5 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/5 (5 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/6 (4 ms)
9: [ RUN ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffQ/PmeSolveTest.ReproducesOutputs/7 (4 ms)
9: [----------] 8 tests from DifferentEwaldCoeffQ/PmeSolveTest (38 ms total)
9:
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/0 (11 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/1 (11 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/2 (6 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/3 (6 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/4 (11 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/5 (10 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/6 (6 ms)
9: [ RUN ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEwaldCoeffLJ/PmeSolveTest.ReproducesOutputs/7 (6 ms)
9: [----------] 8 tests from DifferentEwaldCoeffLJ/PmeSolveTest (68 ms total)
9:
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/0 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/1 (11 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/2 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/3 (11 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/4 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/5 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/6 (3 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/7 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/8 (5 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/9 (10 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/10 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/11 (11 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/12 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/13 (6 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/14 (4 ms)
9: [ RUN ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15
9: [ OK ] DifferentEpsilonR/PmeSolveTest.ReproducesOutputs/15 (6 ms)
9: [----------] 16 tests from DifferentEpsilonR/PmeSolveTest (107 ms total)
9:
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/0 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/1 (11 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/2 (7 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/3 (7 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/4 (42 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/5 (17 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/6 (5 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/7 (6 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/8 (6 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/9 (8 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/10 (17 ms)
9: [ RUN ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput1/PmeSplineAndSpreadTest.ReproducesOutputs/11 (11 ms)
9: [----------] 12 tests from SaneInput1/PmeSplineAndSpreadTest (144 ms total)
9:
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/0 (6 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/1 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/2 (9 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/3 (17 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/4 (20 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/5 (13 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/6 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/7 (7 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/8 (9 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/9 (10 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/10 (13 ms)
9: [ RUN ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput2/PmeSplineAndSpreadTest.ReproducesOutputs/11 (15 ms)
9: [----------] 12 tests from SaneInput2/PmeSplineAndSpreadTest (140 ms total)
9:
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/0 (20 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/1 (18 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/2 (25 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/3 (28 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/4 (37 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/5 (40 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/6 (17 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/7 (18 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/8 (25 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/9 (28 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/10 (33 ms)
9: [ RUN ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11
9: [ OK ] SaneInput13/PmeSplineAndSpreadTest.ReproducesOutputs/11 (64 ms)
9: [----------] 12 tests from SaneInput13/PmeSplineAndSpreadTest (377 ms total)
9:
9: [----------] Global test environment tear-down
9: [==========] 257 tests from 10 test cases ran. (1887 ms total)
9: [ PASSED ] 257 tests.
9/54 Test #9: EwaldUnitTests ...................... Passed 2.15 sec
test 10
Start 10: FFTUnitTests
10: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fft-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FFTUnitTests.xml"
10: Test timeout computed to be: 30
10: [==========] Running 14 tests from 4 test cases.
10: [----------] Global test environment set-up.
10: [----------] 2 tests from ManyFFTTest
10: [ RUN ] ManyFFTTest.Complex1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Complex1DLength48Multi5Test (36 ms)
10: [ RUN ] ManyFFTTest.Real1DLength48Multi5Test
10: [ OK ] ManyFFTTest.Real1DLength48Multi5Test (43 ms)
10: [----------] 2 tests from ManyFFTTest (84 ms total)
10:
10: [----------] 1 test from FFTTest
10: [ RUN ] FFTTest.Real2DLength18_15Test
10: [ OK ] FFTTest.Real2DLength18_15Test (13 ms)
10: [----------] 1 test from FFTTest (14 ms total)
10:
10: [----------] 1 test from FFFTest3D
10: [ RUN ] FFFTest3D.Real5_6_9
10: [ OK ] FFFTest3D.Real5_6_9 (11 ms)
10: [----------] 1 test from FFFTest3D (13 ms total)
10:
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/0 (3 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/1 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/2 (4 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/3 (7 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Complex/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Complex/4 (7 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/0
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/0 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/1
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/1 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/2
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/2 (2 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/3
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/3 (22 ms)
10: [ RUN ] 7_8_25_36_60/FFTTest1D.Real/4
10: [ OK ] 7_8_25_36_60/FFTTest1D.Real/4 (34 ms)
10: [----------] 10 tests from 7_8_25_36_60/FFTTest1D (87 ms total)
10:
10: [----------] Global test environment tear-down
10: [==========] 14 tests from 4 test cases ran. (198 ms total)
10: [ PASSED ] 14 tests.
10/54 Test #10: FFTUnitTests ........................ Passed 0.26 sec
test 11
Start 11: GpuUtilsUnitTests
11: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gpu_utils-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GpuUtilsUnitTests.xml"
11: Test timeout computed to be: 30
11: [==========] Running 62 tests from 20 test cases.
11: [----------] Global test environment set-up.
11: [----------] 2 tests from ClfftInitializer
11: [ RUN ] ClfftInitializer.SingleInitializationWorks
11: [ OK ] ClfftInitializer.SingleInitializationWorks (0 ms)
11: [ RUN ] ClfftInitializer.TwoInitializationsWork
11: [ OK ] ClfftInitializer.TwoInitializationsWork (0 ms)
11: [----------] 2 tests from ClfftInitializer (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/0, where TypeParam = int
11: [ RUN ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/0.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/0.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/0.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/0 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/1, where TypeParam = double
11: [ RUN ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/1.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/1.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/1.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/1 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/2.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/2.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/2.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/2 (0 ms total)
11:
11: [----------] 2 tests from HostAllocatorTest/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks
11: [ OK ] HostAllocatorTest/3.EmptyMemoryAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTest/3.StatefulAllocatorUsesMemory
11: [ OK ] HostAllocatorTest/3.StatefulAllocatorUsesMemory (0 ms)
11: [----------] 2 tests from HostAllocatorTest/3 (0 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/0.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/0.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/0.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/0 (1 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/1.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/1.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/1.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/1 (1 ms total)
11:
11: [----------] 3 tests from HostAllocatorTestCopyable/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks
11: [ OK ] HostAllocatorTestCopyable/2.VectorsWithDefaultHostAllocatorAlwaysWorks (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork
11: [ OK ] HostAllocatorTestCopyable/2.TransfersWithoutPinningWork (0 ms)
11: [ RUN ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve
11: [ OK ] HostAllocatorTestCopyable/2.FillInputAlsoWorksAfterCallingReserve (0 ms)
11: [----------] 3 tests from HostAllocatorTestCopyable/2 (1 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMem/0.CreateVector
11: [ OK ] HostAllocatorTestNoMem/0.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/0.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/0.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Swap
11: [ OK ] HostAllocatorTestNoMem/0.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/0.Comparison
11: [ OK ] HostAllocatorTestNoMem/0.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/0 (2 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestNoMem/1.CreateVector
11: [ OK ] HostAllocatorTestNoMem/1.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/1.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/1.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Swap
11: [ OK ] HostAllocatorTestNoMem/1.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/1.Comparison
11: [ OK ] HostAllocatorTestNoMem/1.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/1 (1 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestNoMem/2.CreateVector
11: [ OK ] HostAllocatorTestNoMem/2.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/2.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/2.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Swap
11: [ OK ] HostAllocatorTestNoMem/2.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/2.Comparison
11: [ OK ] HostAllocatorTestNoMem/2.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/2 (2 ms total)
11:
11: [----------] 5 tests from HostAllocatorTestNoMem/3, where TypeParam = gmx::test::MoveOnly
11: [ RUN ] HostAllocatorTestNoMem/3.CreateVector
11: [ OK ] HostAllocatorTestNoMem/3.CreateVector (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveAssignment
11: [ OK ] HostAllocatorTestNoMem/3.MoveAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.MoveConstruction
11: [ OK ] HostAllocatorTestNoMem/3.MoveConstruction (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Swap
11: [ OK ] HostAllocatorTestNoMem/3.Swap (0 ms)
11: [ RUN ] HostAllocatorTestNoMem/3.Comparison
11: [ OK ] HostAllocatorTestNoMem/3.Comparison (0 ms)
11: [----------] 5 tests from HostAllocatorTestNoMem/3 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0, where TypeParam = int
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/0.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/0.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/0 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1, where TypeParam = double
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/1.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/1.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/1 (1 ms total)
11:
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2, where TypeParam = gmx::BasicVector<double>
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyAssignment
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyAssignment (0 ms)
11: [ RUN ] HostAllocatorTestNoMemCopyable/2.CopyConstruction
11: [ OK ] HostAllocatorTestNoMemCopyable/2.CopyConstruction (0 ms)
11: [----------] 2 tests from HostAllocatorTestNoMemCopyable/2 (0 ms total)
11:
11: [----------] 1 test from HostAllocatorUntypedTest
11: [ RUN ] HostAllocatorUntypedTest.Comparison
11: [ OK ] HostAllocatorUntypedTest.Comparison (0 ms)
11: [----------] 1 test from HostAllocatorUntypedTest (0 ms total)
11:
11: [----------] 4 tests from AllocatorTest/0, where TypeParam = gmx::Allocator<double, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/0.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndResizesWithAlignment (1 ms)
11: [ RUN ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/0.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/0.Move
11: [ OK ] AllocatorTest/0.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/0 (2 ms total)
11:
11: [----------] 4 tests from AllocatorTest/1, where TypeParam = gmx::Allocator<int, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/1.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/1.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/1.Move
11: [ OK ] AllocatorTest/1.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/1 (2 ms total)
11:
11: [----------] 4 tests from AllocatorTest/2, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/2.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndResizesWithAlignment (2 ms)
11: [ RUN ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/2.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/2.Move
11: [ OK ] AllocatorTest/2.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/2 (3 ms total)
11:
11: [----------] 4 tests from AllocatorTest/3, where TypeParam = gmx::Allocator<gmx::test::MoveOnly, gmx::HostAllocationPolicy>
11: [ RUN ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment
11: [ OK ] AllocatorTest/3.AllocatorAlignAllocatesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndResizesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment
11: [ OK ] AllocatorTest/3.VectorAllocatesAndReservesWithAlignment (0 ms)
11: [ RUN ] AllocatorTest/3.Move
11: [ OK ] AllocatorTest/3.Move (0 ms)
11: [----------] 4 tests from AllocatorTest/3 (2 ms total)
11:
11: [----------] Global test environment tear-down
11: [==========] 62 tests from 20 test cases ran. (26 ms total)
11: [ PASSED ] 62 tests.
11/54 Test #11: GpuUtilsUnitTests ................... Passed 0.10 sec
test 12
Start 12: HardwareUnitTests
12: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/hardware-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/HardwareUnitTests.xml"
12: Test timeout computed to be: 30
12: [==========] Running 4 tests from 1 test case.
12: [----------] Global test environment set-up.
12: [----------] 4 tests from HardwareTopologyTest
12: [ RUN ] HardwareTopologyTest.Execute
12: [ OK ] HardwareTopologyTest.Execute (35 ms)
12: [ RUN ] HardwareTopologyTest.HwlocExecute
12: [ OK ] HardwareTopologyTest.HwlocExecute (32 ms)
12: [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency
12: [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (32 ms)
12: [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency
12: [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (32 ms)
12: [----------] 4 tests from HardwareTopologyTest (132 ms total)
12:
12: [----------] Global test environment tear-down
12: [==========] 4 tests from 1 test case ran. (133 ms total)
12: [ PASSED ] 4 tests.
12/54 Test #12: HardwareUnitTests ................... Passed 0.19 sec
test 13
Start 13: MathUnitTests
13: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/math-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MathUnitTests.xml"
13: Test timeout computed to be: 30
13: [==========] Running 204 tests from 29 test cases.
13: [----------] Global test environment set-up.
13: [----------] 1 test from EmptyArrayRefWithPaddingTest
13: [ RUN ] EmptyArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyArrayRefWithPaddingTest (1 ms total)
13:
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest
13: [ RUN ] EmptyConstArrayRefWithPaddingTest.IsEmpty
13: [ OK ] EmptyConstArrayRefWithPaddingTest.IsEmpty (0 ms)
13: [----------] 1 test from EmptyConstArrayRefWithPaddingTest (0 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/0, where TypeParam = gmx::ArrayRefWithPadding<int>
13: [ RUN ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/0.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/0.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/0 (1 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/1, where TypeParam = gmx::ArrayRefWithPadding<float>
13: [ RUN ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/1.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/1.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/1 (1 ms total)
13:
13: [----------] 2 tests from ArrayRefWithPaddingTest/2, where TypeParam = gmx::ArrayRefWithPadding<double>
13: [ RUN ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks
13: [ OK ] ArrayRefWithPaddingTest/2.AssignFromPaddedVectorWorks (0 ms)
13: [ RUN ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks
13: [ OK ] ArrayRefWithPaddingTest/2.ConstructFromPointersWorks (0 ms)
13: [----------] 2 tests from ArrayRefWithPaddingTest/2 (1 ms total)
13:
13: [----------] 8 tests from TranslateAndScaleTest
13: [ RUN ] TranslateAndScaleTest.identityTransformation
13: [ OK ] TranslateAndScaleTest.identityTransformation (1 ms)
13: [ RUN ] TranslateAndScaleTest.translationWithIdentityScaling
13: [ OK ] TranslateAndScaleTest.translationWithIdentityScaling (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingWithZeroTranslation
13: [ OK ] TranslateAndScaleTest.scalingWithZeroTranslation (0 ms)
13: [ RUN ] TranslateAndScaleTest.translationAndScalingNonTrivial
13: [ OK ] TranslateAndScaleTest.translationAndScalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingIdentity
13: [ OK ] TranslateAndScaleTest.scalingIdentity (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingNonTrivial
13: [ OK ] TranslateAndScaleTest.scalingNonTrivial (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseNoZero
13: [ OK ] TranslateAndScaleTest.scalingInverseNoZero (0 ms)
13: [ RUN ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero
13: [ OK ] TranslateAndScaleTest.scalingInverseWithOneScaleDimensionZero (0 ms)
13: [----------] 8 tests from TranslateAndScaleTest (4 ms total)
13:
13: [----------] 12 tests from DensitySimilarityTest
13: [ RUN ] DensitySimilarityTest.InnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductIsCorrect (1 ms)
13: [ RUN ] DensitySimilarityTest.InnerProductGradientIsCorrect
13: [ OK ] DensitySimilarityTest.InnerProductGradientIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.GradientThrowsIfDensitiesDontMatch (1 ms)
13: [ RUN ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch
13: [ OK ] DensitySimilarityTest.SimilarityThrowsIfDensitiesDontMatch (0 ms)
13: [ RUN ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect
13: [ OK ] DensitySimilarityTest.CopiedMeasureInnerProductIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero
13: [ OK ] DensitySimilarityTest.RelativeEntropyOfSameDensityIsZero (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect
13: [ OK ] DensitySimilarityTest.RelativeEntropyGradientIsCorrect (0 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsOne
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsOne (183 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationIsMinusOneWhenAntiCorrelated (194 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsZeroWhenCorrelated (121 ms)
13: [ RUN ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect
13: [ OK ] DensitySimilarityTest.CrossCorrelationGradientIsCorrect (0 ms)
13: [----------] 12 tests from DensitySimilarityTest (507 ms total)
13:
13: [----------] 6 tests from StructureSimilarityTest
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho
13: [ OK ] StructureSimilarityTest.StructureComparedToSelfHasZeroRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSD
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSD (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRho
13: [ OK ] StructureSimilarityTest.YieldsCorrectRho (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRMSDWithIndex (0 ms)
13: [ RUN ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex
13: [ OK ] StructureSimilarityTest.YieldsCorrectRhoWidthIndex (0 ms)
13: [----------] 6 tests from StructureSimilarityTest (2 ms total)
13:
13: [----------] 8 tests from ExponentialMovingAverage
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsZero (0 ms)
13: [ RUN ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative
13: [ OK ] ExponentialMovingAverage.ThrowsWhenLagTimeIsNegative (0 ms)
13: [ RUN ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue
13: [ OK ] ExponentialMovingAverage.LagTimeOneYieldsInstantaneousValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.YieldsCorrectValue
13: [ OK ] ExponentialMovingAverage.YieldsCorrectValue (0 ms)
13: [ RUN ] ExponentialMovingAverage.SetAverageCorrectly
13: [ OK ] ExponentialMovingAverage.SetAverageCorrectly (0 ms)
13: [ RUN ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing
13: [ OK ] ExponentialMovingAverage.DeterminesCorrectlyIfIncreasing (0 ms)
13: [ RUN ] ExponentialMovingAverage.InverseLagTimeCorrect
13: [ OK ] ExponentialMovingAverage.InverseLagTimeCorrect (0 ms)
13: [ RUN ] ExponentialMovingAverage.RoundTripAsKeyValueTree
13: [ OK ] ExponentialMovingAverage.RoundTripAsKeyValueTree (0 ms)
13: [----------] 8 tests from ExponentialMovingAverage (1 ms total)
13:
13: [----------] 21 tests from FunctionTest
13: [ RUN ] FunctionTest.StaticLog2
13: [ OK ] FunctionTest.StaticLog2 (0 ms)
13: [ RUN ] FunctionTest.Log2I32Bit
13: [ OK ] FunctionTest.Log2I32Bit (1 ms)
13: [ RUN ] FunctionTest.Log2I64Bit
13: [ OK ] FunctionTest.Log2I64Bit (1 ms)
13: [ RUN ] FunctionTest.GreatestCommonDivisor
13: [ OK ] FunctionTest.GreatestCommonDivisor (0 ms)
13: [ RUN ] FunctionTest.InvsqrtFloat
13: [ OK ] FunctionTest.InvsqrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvsqrtDouble
13: [ OK ] FunctionTest.InvsqrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvsqrtInteger
13: [ OK ] FunctionTest.InvsqrtInteger (0 ms)
13: [ RUN ] FunctionTest.InvcbrtFloat
13: [ OK ] FunctionTest.InvcbrtFloat (0 ms)
13: [ RUN ] FunctionTest.InvcbrtDouble
13: [ OK ] FunctionTest.InvcbrtDouble (0 ms)
13: [ RUN ] FunctionTest.InvcbrtInteger
13: [ OK ] FunctionTest.InvcbrtInteger (0 ms)
13: [ RUN ] FunctionTest.SixthrootFloat
13: [ OK ] FunctionTest.SixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.SixthrootDouble
13: [ OK ] FunctionTest.SixthrootDouble (1 ms)
13: [ RUN ] FunctionTest.SixthrootInteger
13: [ OK ] FunctionTest.SixthrootInteger (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootFloat
13: [ OK ] FunctionTest.InvsixthrootFloat (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootDouble
13: [ OK ] FunctionTest.InvsixthrootDouble (0 ms)
13: [ RUN ] FunctionTest.InvsixthrootInteger
13: [ OK ] FunctionTest.InvsixthrootInteger (1 ms)
13: [ RUN ] FunctionTest.Powers
13: [ OK ] FunctionTest.Powers (0 ms)
13: [ RUN ] FunctionTest.ErfInvFloat
13: [ OK ] FunctionTest.ErfInvFloat (0 ms)
13: [ RUN ] FunctionTest.ErfInvDouble
13: [ OK ] FunctionTest.ErfInvDouble (0 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesFloat
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesFloat (1 ms)
13: [ RUN ] FunctionTest.ErfAndErfInvAreInversesDouble
13: [ OK ] FunctionTest.ErfAndErfInvAreInversesDouble (1 ms)
13: [----------] 21 tests from FunctionTest (11 ms total)
13:
13: [----------] 4 tests from GaussianOn1DLattice
13: [ RUN ] GaussianOn1DLattice.sumsCloseToOne
13: [ OK ] GaussianOn1DLattice.sumsCloseToOne (0 ms)
13: [ RUN ] GaussianOn1DLattice.isCorrect
13: [ OK ] GaussianOn1DLattice.isCorrect (0 ms)
13: [ RUN ] GaussianOn1DLattice.complementaryAmplitudesSumToZero
13: [ OK ] GaussianOn1DLattice.complementaryAmplitudesSumToZero (1 ms)
13: [ RUN ] GaussianOn1DLattice.doesNotOverflowForLargeRange
13: [ OK ] GaussianOn1DLattice.doesNotOverflowForLargeRange (0 ms)
13: [----------] 4 tests from GaussianOn1DLattice (1 ms total)
13:
13: [----------] 9 tests from GaussTransformTest
13: [ RUN ] GaussTransformTest.isZeroUponConstruction
13: [ OK ] GaussTransformTest.isZeroUponConstruction (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss
13: [ OK ] GaussTransformTest.isZeroAddingZeroAmplitudeGauss (0 ms)
13: [ RUN ] GaussTransformTest.isZeroAfterSettingZero
13: [ OK ] GaussTransformTest.isZeroAfterSettingZero (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinX
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinX (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinY
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinY (0 ms)
13: [ RUN ] GaussTransformTest.isZeroWhenOutsideRangeinZ
13: [ OK ] GaussTransformTest.isZeroWhenOutsideRangeinZ (0 ms)
13: [ RUN ] GaussTransformTest.complementaryGaussAddToZero
13: [ OK ] GaussTransformTest.complementaryGaussAddToZero (0 ms)
13: [ RUN ] GaussTransformTest.centerGaussianInCubeHasExpectedValues
13: [ OK ] GaussTransformTest.centerGaussianInCubeHasExpectedValues (1 ms)
13: [ RUN ] GaussTransformTest.view
13: [ OK ] GaussTransformTest.view (0 ms)
13: [----------] 9 tests from GaussTransformTest (1 ms total)
13:
13: [----------] 3 tests from DensityFittingForce
13: [ RUN ] DensityFittingForce.isZeroWhenMatchingDensity
13: [ OK ] DensityFittingForce.isZeroWhenMatchingDensity (0 ms)
13: [ RUN ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections
13: [ OK ] DensityFittingForce.isZeroWhenMismatchingSameAllDirections (1 ms)
13: [ RUN ] DensityFittingForce.pullsTowardsDerivative
13: [ OK ] DensityFittingForce.pullsTowardsDerivative (0 ms)
13: [----------] 3 tests from DensityFittingForce (1 ms total)
13:
13: [----------] 2 tests from InvertMatrixTest
13: [ RUN ] InvertMatrixTest.IdentityIsImpotent
13: [ OK ] InvertMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertMatrixTest.ComputesInverse
13: [ OK ] InvertMatrixTest.ComputesInverse (0 ms)
13: [----------] 2 tests from InvertMatrixTest (0 ms total)
13:
13: [----------] 2 tests from InvertBoxMatrixTest
13: [ RUN ] InvertBoxMatrixTest.IdentityIsImpotent
13: [ OK ] InvertBoxMatrixTest.IdentityIsImpotent (0 ms)
13: [ RUN ] InvertBoxMatrixTest.ComputesInverseInPlace
13: [ OK ] InvertBoxMatrixTest.ComputesInverseInPlace (0 ms)
13: [----------] 2 tests from InvertBoxMatrixTest (0 ms total)
13:
13: [----------] 15 tests from MatrixTest
13: [ RUN ] MatrixTest.canSetFromArray
13: [ OK ] MatrixTest.canSetFromArray (0 ms)
13: [ RUN ] MatrixTest.canSetStaticallyFromList
13: [ OK ] MatrixTest.canSetStaticallyFromList (0 ms)
13: [ RUN ] MatrixTest.canConstructAndFill
13: [ OK ] MatrixTest.canConstructAndFill (0 ms)
13: [ RUN ] MatrixTest.canSetValues
13: [ OK ] MatrixTest.canSetValues (0 ms)
13: [ RUN ] MatrixTest.canCopyAssign
13: [ OK ] MatrixTest.canCopyAssign (1 ms)
13: [ RUN ] MatrixTest.canSwap
13: [ OK ] MatrixTest.canSwap (0 ms)
13: [ RUN ] MatrixTest.staticMultiDimArrayExtent
13: [ OK ] MatrixTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MatrixTest.determinantWorks
13: [ OK ] MatrixTest.determinantWorks (0 ms)
13: [ RUN ] MatrixTest.noninvertableDeterminantIsZero
13: [ OK ] MatrixTest.noninvertableDeterminantIsZero (0 ms)
13: [ RUN ] MatrixTest.determinantOfDiagonalMatrix
13: [ OK ] MatrixTest.determinantOfDiagonalMatrix (0 ms)
13: [ RUN ] MatrixTest.traceWorks
13: [ OK ] MatrixTest.traceWorks (0 ms)
13: [ RUN ] MatrixTest.transposeWorks
13: [ OK ] MatrixTest.transposeWorks (0 ms)
13: [ RUN ] MatrixTest.transposeOfSymmetricMatrix
13: [ OK ] MatrixTest.transposeOfSymmetricMatrix (0 ms)
13: [ RUN ] MatrixTest.canCreateFromLegacyMatrix
13: [ OK ] MatrixTest.canCreateFromLegacyMatrix (0 ms)
13: [ RUN ] MatrixTest.canFillLegacyMatrix
13: [ OK ] MatrixTest.canFillLegacyMatrix (0 ms)
13: [----------] 15 tests from MatrixTest (1 ms total)
13:
13: [----------] 25 tests from MultiDimArrayTest
13: [ RUN ] MultiDimArrayTest.canConstructAndFillStatic
13: [ OK ] MultiDimArrayTest.canConstructAndFillStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canConstructAndFillDynamic
13: [ OK ] MultiDimArrayTest.canConstructAndFillDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInStatic
13: [ OK ] MultiDimArrayTest.canSetValuesInStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSetValuesInDynamic
13: [ OK ] MultiDimArrayTest.canSetValuesInDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructStatic
13: [ OK ] MultiDimArrayTest.canMoveConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveConstructDynamic
13: [ OK ] MultiDimArrayTest.canMoveConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignStatic
13: [ OK ] MultiDimArrayTest.canMoveAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canMoveAssignDynamic
13: [ OK ] MultiDimArrayTest.canMoveAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructStatic
13: [ OK ] MultiDimArrayTest.canCopyConstructStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyConstructDynamic
13: [ OK ] MultiDimArrayTest.canCopyConstructDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignStatic
13: [ OK ] MultiDimArrayTest.canCopyAssignStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canCopyAssignDynamic
13: [ OK ] MultiDimArrayTest.canCopyAssignDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapStatic
13: [ OK ] MultiDimArrayTest.canSwapStatic (0 ms)
13: [ RUN ] MultiDimArrayTest.canSwapDynamic
13: [ OK ] MultiDimArrayTest.canSwapDynamic (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizesToCorrectExtent (0 ms)
13: [ RUN ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue
13: [ OK ] MultiDimArrayTest.dynamicMultiDimArrayResizeAndSetValue (0 ms)
13: [ RUN ] MultiDimArrayTest.staticMultiDimArrayFromArray
13: [ OK ] MultiDimArrayTest.staticMultiDimArrayFromArray (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToView
13: [ OK ] MultiDimArrayTest.conversionToView (0 ms)
13: [ RUN ] MultiDimArrayTest.conversionToConstView
13: [ OK ] MultiDimArrayTest.conversionToConstView (0 ms)
13: [ RUN ] MultiDimArrayTest.viewBegin
13: [ OK ] MultiDimArrayTest.viewBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.viewEnd
13: [ OK ] MultiDimArrayTest.viewEnd (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstBegin
13: [ OK ] MultiDimArrayTest.constViewConstBegin (0 ms)
13: [ RUN ] MultiDimArrayTest.constViewConstEnd
13: [ OK ] MultiDimArrayTest.constViewConstEnd (0 ms)
13: [----------] 25 tests from MultiDimArrayTest (1 ms total)
13:
13: [----------] 4 tests from MultiDimArrayToMdSpanTest
13: [ RUN ] MultiDimArrayToMdSpanTest.convertsToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.convertsToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.constArrayToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.constArrayToMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.nonConstArrayToConstMdSpan (0 ms)
13: [ RUN ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan
13: [ OK ] MultiDimArrayToMdSpanTest.implicitConversionToMdSpan (0 ms)
13: [----------] 4 tests from MultiDimArrayToMdSpanTest (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/0, where TypeParam = std::allocator<int>
13: [ RUN ] PaddedVectorTest/0.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/0.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanCopyAssign
13: [ OK ] PaddedVectorTest/0.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanMoveAssign
13: [ OK ] PaddedVectorTest/0.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/0.CanSwap
13: [ OK ] PaddedVectorTest/0.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/0 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/1, where TypeParam = std::allocator<float>
13: [ RUN ] PaddedVectorTest/1.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/1.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanCopyAssign
13: [ OK ] PaddedVectorTest/1.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanMoveAssign
13: [ OK ] PaddedVectorTest/1.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/1.CanSwap
13: [ OK ] PaddedVectorTest/1.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/1 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/2, where TypeParam = std::allocator<double>
13: [ RUN ] PaddedVectorTest/2.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/2.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanCopyAssign
13: [ OK ] PaddedVectorTest/2.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanMoveAssign
13: [ OK ] PaddedVectorTest/2.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/2.CanSwap
13: [ OK ] PaddedVectorTest/2.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/2 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/3, where TypeParam = std::allocator<gmx::BasicVector<float> >
13: [ RUN ] PaddedVectorTest/3.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/3.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanCopyAssign
13: [ OK ] PaddedVectorTest/3.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanMoveAssign
13: [ OK ] PaddedVectorTest/3.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/3.CanSwap
13: [ OK ] PaddedVectorTest/3.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/3 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/4, where TypeParam = std::allocator<gmx::BasicVector<double> >
13: [ RUN ] PaddedVectorTest/4.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/4.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanCopyAssign
13: [ OK ] PaddedVectorTest/4.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanMoveAssign
13: [ OK ] PaddedVectorTest/4.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/4.CanSwap
13: [ OK ] PaddedVectorTest/4.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/4 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/5, where TypeParam = gmx::Allocator<int, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/5.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/5.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanCopyAssign
13: [ OK ] PaddedVectorTest/5.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanMoveAssign
13: [ OK ] PaddedVectorTest/5.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/5.CanSwap
13: [ OK ] PaddedVectorTest/5.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/5 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/6, where TypeParam = gmx::Allocator<float, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/6.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/6.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanCopyAssign
13: [ OK ] PaddedVectorTest/6.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanMoveAssign
13: [ OK ] PaddedVectorTest/6.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/6.CanSwap
13: [ OK ] PaddedVectorTest/6.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/6 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/7, where TypeParam = gmx::Allocator<double, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/7.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/7.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanCopyAssign
13: [ OK ] PaddedVectorTest/7.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/7.CanMoveAssign
13: [ OK ] PaddedVectorTest/7.CanMoveAssign (1 ms)
13: [ RUN ] PaddedVectorTest/7.CanSwap
13: [ OK ] PaddedVectorTest/7.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/7 (1 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/8, where TypeParam = gmx::Allocator<gmx::BasicVector<float>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/8.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/8.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanCopyAssign
13: [ OK ] PaddedVectorTest/8.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanMoveAssign
13: [ OK ] PaddedVectorTest/8.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/8.CanSwap
13: [ OK ] PaddedVectorTest/8.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/8 (0 ms total)
13:
13: [----------] 4 tests from PaddedVectorTest/9, where TypeParam = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>
13: [ RUN ] PaddedVectorTest/9.ConstructsResizesAndReserves
13: [ OK ] PaddedVectorTest/9.ConstructsResizesAndReserves (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanCopyAssign
13: [ OK ] PaddedVectorTest/9.CanCopyAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanMoveAssign
13: [ OK ] PaddedVectorTest/9.CanMoveAssign (0 ms)
13: [ RUN ] PaddedVectorTest/9.CanSwap
13: [ OK ] PaddedVectorTest/9.CanSwap (0 ms)
13: [----------] 4 tests from PaddedVectorTest/9 (0 ms total)
13:
13: [----------] 37 tests from RVecTest
13: [ RUN ] RVecTest.CanBeStoredInVector
13: [ OK ] RVecTest.CanBeStoredInVector (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyFrom_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyFrom_rvec (0 ms)
13: [ RUN ] RVecTest.ConvertsImplicitlyTo_rvec
13: [ OK ] RVecTest.ConvertsImplicitlyTo_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAsMutable_rvec
13: [ OK ] RVecTest.WorksAsMutable_rvec (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Array
13: [ OK ] RVecTest.WorksAs_rvec_Array (0 ms)
13: [ RUN ] RVecTest.CanAddRVecToRvec
13: [ OK ] RVecTest.CanAddRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanAddAssignRVecToRvec
13: [ OK ] RVecTest.CanAddAssignRVecToRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractRVecFromRvec
13: [ OK ] RVecTest.CanSubtractRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanSubtractAssignRVecFromRvec
13: [ OK ] RVecTest.CanSubtractAssignRVecFromRvec (0 ms)
13: [ RUN ] RVecTest.CanDotProductRVecByRvec
13: [ OK ] RVecTest.CanDotProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanCrossProductRVecByRvec
13: [ OK ] RVecTest.CanCrossProductRVecByRvec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVecInplace
13: [ OK ] RVecTest.CanDivideRVecInplace (0 ms)
13: [ RUN ] RVecTest.CanScaleRVec
13: [ OK ] RVecTest.CanScaleRVec (0 ms)
13: [ RUN ] RVecTest.CanDivideRVec
13: [ OK ] RVecTest.CanDivideRVec (0 ms)
13: [ RUN ] RVecTest.CanDoUnitvFromRVec
13: [ OK ] RVecTest.CanDoUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanSqLengthOfRVec
13: [ OK ] RVecTest.CanSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanLengthOfRVec
13: [ OK ] RVecTest.CanLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToRVec
13: [ OK ] RVecTest.CanCastToRVec (0 ms)
13: [ RUN ] RVecTest.CanCastToDVec
13: [ OK ] RVecTest.CanCastToDVec (0 ms)
13: [ RUN ] RVecTest.CanLeftScalarMultiply
13: [ OK ] RVecTest.CanLeftScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanRightScalarMultiply
13: [ OK ] RVecTest.CanRightScalarMultiply (0 ms)
13: [ RUN ] RVecTest.CanGetUnitvFromRVec
13: [ OK ] RVecTest.CanGetUnitvFromRVec (0 ms)
13: [ RUN ] RVecTest.CanGetSqLengthOfRVec
13: [ OK ] RVecTest.CanGetSqLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanGetLengthOfRVec
13: [ OK ] RVecTest.CanGetLengthOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoCrossProductOfRVec
13: [ OK ] RVecTest.CanDoCrossProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanDoDotProductOfRVec
13: [ OK ] RVecTest.CanDoDotProductOfRVec (0 ms)
13: [ RUN ] RVecTest.CanScaleByVector
13: [ OK ] RVecTest.CanScaleByVector (0 ms)
13: [ RUN ] RVecTest.asIVec
13: [ OK ] RVecTest.asIVec (0 ms)
13: [ RUN ] RVecTest.elementWiseMin
13: [ OK ] RVecTest.elementWiseMin (0 ms)
13: [ RUN ] RVecTest.elementWiseMax
13: [ OK ] RVecTest.elementWiseMax (0 ms)
13: [ RUN ] RVecTest.WorksAs_dvec_Reference
13: [ OK ] RVecTest.WorksAs_dvec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_ivec_Reference
13: [ OK ] RVecTest.WorksAs_ivec_Reference (0 ms)
13: [ RUN ] RVecTest.WorksAs_rvec_Reference
13: [ OK ] RVecTest.WorksAs_rvec_Reference (0 ms)
13: [ RUN ] RVecTest.CopyConstructorWorks
13: [ OK ] RVecTest.CopyConstructorWorks (0 ms)
13: [ RUN ] RVecTest.CopyAssignmentWorks
13: [ OK ] RVecTest.CopyAssignmentWorks (0 ms)
13: [ RUN ] RVecTest.MoveConstructorWorks
13: [ OK ] RVecTest.MoveConstructorWorks (0 ms)
13: [ RUN ] RVecTest.MoveAssignmentWorks
13: [ OK ] RVecTest.MoveAssignmentWorks (0 ms)
13: [----------] 37 tests from RVecTest (2 ms total)
13:
13: [----------] Global test environment tear-down
13: [==========] 204 tests from 29 test cases ran. (543 ms total)
13: [ PASSED ] 204 tests.
13/54 Test #13: MathUnitTests ....................... Passed 0.65 sec
test 14
Start 14: MdrunUtilityUnitTests
14: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityUnitTests.xml"
14: Test timeout computed to be: 30
14: [==========] Running 17 tests from 1 test case.
14: [----------] Global test environment set-up.
14: [----------] 17 tests from ThreadAffinityTest
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenDisabled
14: [ OK ] ThreadAffinityTest.DoesNothingWhenDisabled (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWhenNotSupported
14: [ OK ] ThreadAffinityTest.DoesNothingWhenNotSupported (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooFewUserSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyUserSetThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithAutoAndTooManyAutoSetThreads (0 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithUnknownHardware
14: [ OK ] ThreadAffinityTest.DoesNothingWithUnknownHardware (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooManyThreads
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooManyThreads (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeOffset
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeOffset (1 ms)
14: [ RUN ] ThreadAffinityTest.DoesNothingWithTooLargeStride
14: [ OK ] ThreadAffinityTest.DoesNothingWithTooLargeStride (0 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithAuto
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithAuto (2 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced
14: [ OK ] ThreadAffinityTest.PinsSingleThreadWithOffsetWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread
14: NOTE: Affinity setting failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithSingleThread (2 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithAuto
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithAuto (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced
14: [ OK ] ThreadAffinityTest.PinsMultipleThreadsWithStrideWhenForced (1 ms)
14: [ RUN ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads
14: [ OK ] ThreadAffinityTest.PinsWithAutoAndFewerAutoSetThreads (2 ms)
14: [ RUN ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing
14: NOTE: Affinity setting for 1/2 threads failed.
14: [ OK ] ThreadAffinityTest.HandlesPinningFailureWithOneThreadFailing (1 ms)
14: [----------] 17 tests from ThreadAffinityTest (18 ms total)
14:
14: [----------] Global test environment tear-down
14: [==========] 17 tests from 1 test case ran. (18 ms total)
14: [ PASSED ] 17 tests.
14/54 Test #14: MdrunUtilityUnitTests ............... Passed 0.08 sec
test 15
Start 15: MdrunUtilityMpiUnitTests
15: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrunutility-mpi-test "-ntmpi" "4" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunUtilityMpiUnitTests.xml"
15: Test timeout computed to be: 30
15: [==========] Running 13 tests from 2 test cases.
15: [----------] Global test environment set-up.
15: [----------] 6 tests from ThreadAffinityMultiRankTest
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWholeNode
15: [ OK ] ThreadAffinityMultiRankTest.PinsWholeNode (41 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride
15: [ OK ] ThreadAffinityMultiRankTest.PinsWithOffsetAndStride (51 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.PinsTwoNodes
15: [ OK ] ThreadAffinityMultiRankTest.PinsTwoNodes (8 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled
15: [ OK ] ThreadAffinityMultiRankTest.DoesNothingWhenDisabled (2 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithAuto (3 ms)
15: [ RUN ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce
15: [ OK ] ThreadAffinityMultiRankTest.HandlesTooManyThreadsWithForce (3 ms)
15: [----------] 6 tests from ThreadAffinityMultiRankTest (108 ms total)
15:
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsOnNonMasterOnly (3 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesUnknownHardwareOnNonMaster (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.PinsAutomaticallyOnNonMasterOnly (4 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidOffsetOnNonMasterOnly (5 ms)
15: [ RUN ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly
15: [ OK ] ThreadAffinityHeterogeneousNodesTest.HandlesInvalidStrideOnNonMasterOnly (4 ms)
15: [----------] 7 tests from ThreadAffinityHeterogeneousNodesTest (31 ms total)
15:
15: [----------] Global test environment tear-down
15: [==========] 13 tests from 2 test cases ran. (139 ms total)
15: [ PASSED ] 13 tests.
15/54 Test #15: MdrunUtilityMpiUnitTests ............ Passed 0.23 sec
test 16
Start 16: MDSpanTests
16: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdspan-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MDSpanTests.xml"
16: Test timeout computed to be: 30
16: [==========] Running 32 tests from 7 test cases.
16: [----------] Global test environment set-up.
16: [----------] 4 tests from BasicAccessorPolicy
16: [ RUN ] BasicAccessorPolicy.Decay
16: [ OK ] BasicAccessorPolicy.Decay (0 ms)
16: [ RUN ] BasicAccessorPolicy.Access
16: [ OK ] BasicAccessorPolicy.Access (0 ms)
16: [ RUN ] BasicAccessorPolicy.Offset
16: [ OK ] BasicAccessorPolicy.Offset (0 ms)
16: [ RUN ] BasicAccessorPolicy.CopyAccessor
16: [ OK ] BasicAccessorPolicy.CopyAccessor (0 ms)
16: [----------] 4 tests from BasicAccessorPolicy (1 ms total)
16:
16: [----------] 4 tests from ExtentsTest
16: [ RUN ] ExtentsTest.Construction
16: [ OK ] ExtentsTest.Construction (0 ms)
16: [ RUN ] ExtentsTest.PurelyStatic
16: [ OK ] ExtentsTest.PurelyStatic (0 ms)
16: [ RUN ] ExtentsTest.RankNought
16: [ OK ] ExtentsTest.RankNought (0 ms)
16: [ RUN ] ExtentsTest.Assignment
16: [ OK ] ExtentsTest.Assignment (0 ms)
16: [----------] 4 tests from ExtentsTest (1 ms total)
16:
16: [----------] 8 tests from MdSpanExtension
16: [ RUN ] MdSpanExtension.SlicingAllStatic
16: [ OK ] MdSpanExtension.SlicingAllStatic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingDynamic
16: [ OK ] MdSpanExtension.SlicingDynamic (0 ms)
16: [ RUN ] MdSpanExtension.SlicingAllStatic3D
16: [ OK ] MdSpanExtension.SlicingAllStatic3D (0 ms)
16: [ RUN ] MdSpanExtension.SlicingEqualsView3D
16: [ OK ] MdSpanExtension.SlicingEqualsView3D (0 ms)
16: [ RUN ] MdSpanExtension.additionWorks
16: [ OK ] MdSpanExtension.additionWorks (0 ms)
16: [ RUN ] MdSpanExtension.subtractionWorks
16: [ OK ] MdSpanExtension.subtractionWorks (0 ms)
16: [ RUN ] MdSpanExtension.multiplicationWorks
16: [ OK ] MdSpanExtension.multiplicationWorks (0 ms)
16: [ RUN ] MdSpanExtension.divisionWorks
16: [ OK ] MdSpanExtension.divisionWorks (0 ms)
16: [----------] 8 tests from MdSpanExtension (0 ms total)
16:
16: [----------] 3 tests from LayoutTests
16: [ RUN ] LayoutTests.LayoutRightConstruction
16: [ OK ] LayoutTests.LayoutRightConstruction (0 ms)
16: [ RUN ] LayoutTests.LayoutRightProperties
16: [ OK ] LayoutTests.LayoutRightProperties (0 ms)
16: [ RUN ] LayoutTests.LayoutRightOperator
16: [ OK ] LayoutTests.LayoutRightOperator (0 ms)
16: [----------] 3 tests from LayoutTests (0 ms total)
16:
16: [----------] 1 test from MdSpanTest
16: [ RUN ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly
16: [ OK ] MdSpanTest.MdSpanWrapsBasicMdSpanCorrectly (0 ms)
16: [----------] 1 test from MdSpanTest (0 ms total)
16:
16: [----------] 6 tests from MdSpanTest/0, where TypeParam = gmx::basic_mdspan<int, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<int> >
16: [ RUN ] MdSpanTest/0.Rank
16: [ OK ] MdSpanTest/0.Rank (0 ms)
16: [ RUN ] MdSpanTest/0.DynamicRank
16: [ OK ] MdSpanTest/0.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/0.Extents
16: [ OK ] MdSpanTest/0.Extents (0 ms)
16: [ RUN ] MdSpanTest/0.Strides
16: [ OK ] MdSpanTest/0.Strides (0 ms)
16: [ RUN ] MdSpanTest/0.Properties
16: [ OK ] MdSpanTest/0.Properties (0 ms)
16: [ RUN ] MdSpanTest/0.Operator
16: [ OK ] MdSpanTest/0.Operator (0 ms)
16: [----------] 6 tests from MdSpanTest/0 (1 ms total)
16:
16: [----------] 6 tests from MdSpanTest/1, where TypeParam = gmx::basic_mdspan<float, gmx::extents<5, -1, 3, -1, 1>, gmx::layout_right, gmx::accessor_basic<float> >
16: [ RUN ] MdSpanTest/1.Rank
16: [ OK ] MdSpanTest/1.Rank (0 ms)
16: [ RUN ] MdSpanTest/1.DynamicRank
16: [ OK ] MdSpanTest/1.DynamicRank (0 ms)
16: [ RUN ] MdSpanTest/1.Extents
16: [ OK ] MdSpanTest/1.Extents (0 ms)
16: [ RUN ] MdSpanTest/1.Strides
16: [ OK ] MdSpanTest/1.Strides (0 ms)
16: [ RUN ] MdSpanTest/1.Properties
16: [ OK ] MdSpanTest/1.Properties (0 ms)
16: [ RUN ] MdSpanTest/1.Operator
16: [ OK ] MdSpanTest/1.Operator (1 ms)
16: [----------] 6 tests from MdSpanTest/1 (1 ms total)
16:
16: [----------] Global test environment tear-down
16: [==========] 32 tests from 7 test cases ran. (4 ms total)
16: [ PASSED ] 32 tests.
16/54 Test #16: MDSpanTests ......................... Passed 0.07 sec
test 17
Start 17: OnlineHelpUnitTests
17: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/onlinehelp-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OnlineHelpUnitTests.xml"
17: Test timeout computed to be: 30
17: [==========] Running 22 tests from 4 test cases.
17: [----------] Global test environment set-up.
17: [----------] 6 tests from TextTableFormatterTest
17: [ RUN ] TextTableFormatterTest.HandlesBasicCase
17: [ OK ] TextTableFormatterTest.HandlesBasicCase (2 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumnTitles
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumnTitles (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesIndentation
17: [ OK ] TextTableFormatterTest.HandlesIndentation (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesOverflowingLines
17: [ OK ] TextTableFormatterTest.HandlesOverflowingLines (0 ms)
17: [ RUN ] TextTableFormatterTest.HandlesLastColumnFolding
17: [ OK ] TextTableFormatterTest.HandlesLastColumnFolding (1 ms)
17: [ RUN ] TextTableFormatterTest.HandlesEmptyColumns
17: [ OK ] TextTableFormatterTest.HandlesEmptyColumns (0 ms)
17: [----------] 6 tests from TextTableFormatterTest (4 ms total)
17:
17: [----------] 3 tests from HelpManagerTest
17: [ RUN ] HelpManagerTest.HandlesRootTopic
17: [ OK ] HelpManagerTest.HandlesRootTopic (1 ms)
17: [ RUN ] HelpManagerTest.HandlesSubTopics
17: [ OK ] HelpManagerTest.HandlesSubTopics (1 ms)
17: [ RUN ] HelpManagerTest.HandlesInvalidTopics
17: [ OK ] HelpManagerTest.HandlesInvalidTopics (0 ms)
17: [----------] 3 tests from HelpManagerTest (2 ms total)
17:
17: [----------] 2 tests from HelpTopicFormattingTest
17: [ RUN ] HelpTopicFormattingTest.FormatsSimpleTopic
17: [ OK ] HelpTopicFormattingTest.FormatsSimpleTopic (0 ms)
17: [ RUN ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics
17: [ OK ] HelpTopicFormattingTest.FormatsCompositeTopicWithSubTopics (1 ms)
17: [----------] 2 tests from HelpTopicFormattingTest (1 ms total)
17:
17: [----------] 11 tests from HelpWriterContextTest
17: [ RUN ] HelpWriterContextTest.FormatsParagraphs
17: [ OK ] HelpWriterContextTest.FormatsParagraphs (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsRstStyleParagraphs
17: [ OK ] HelpWriterContextTest.FormatsRstStyleParagraphs (0 ms)
17: [ RUN ] HelpWriterContextTest.CleansUpExtraWhitespace
17: [ OK ] HelpWriterContextTest.CleansUpExtraWhitespace (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralText
17: [ OK ] HelpWriterContextTest.FormatsLiteralText (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextAtBeginning
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextAtBeginning (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsLiteralTextWithIndentation
17: [ OK ] HelpWriterContextTest.FormatsLiteralTextWithIndentation (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsBulletList
17: [ OK ] HelpWriterContextTest.FormatsBulletList (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsEnumeratedList
17: [ OK ] HelpWriterContextTest.FormatsEnumeratedList (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsSimpleTable
17: [ OK ] HelpWriterContextTest.FormatsSimpleTable (0 ms)
17: [ RUN ] HelpWriterContextTest.FormatsGridTable
17: [ OK ] HelpWriterContextTest.FormatsGridTable (1 ms)
17: [ RUN ] HelpWriterContextTest.FormatsTitles
17: [ OK ] HelpWriterContextTest.FormatsTitles (0 ms)
17: [----------] 11 tests from HelpWriterContextTest (7 ms total)
17:
17: [----------] Global test environment tear-down
17: [==========] 22 tests from 4 test cases ran. (15 ms total)
17: [ PASSED ] 22 tests.
17/54 Test #17: OnlineHelpUnitTests ................. Passed 0.08 sec
test 18
Start 18: OptionsUnitTests
18: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/options-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/OptionsUnitTests.xml"
18: Test timeout computed to be: 30
18: [==========] Running 110 tests from 18 test cases.
18: [----------] Global test environment set-up.
18: [----------] 5 tests from AbstractOptionStorageTest
18: [ RUN ] AbstractOptionStorageTest.HandlesSetInFinish
18: [ OK ] AbstractOptionStorageTest.HandlesSetInFinish (1 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueRemoval
18: [ OK ] AbstractOptionStorageTest.HandlesValueRemoval (0 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesValueAddition (1 ms)
18: [ RUN ] AbstractOptionStorageTest.HandlesTooManyValueAddition
18: [ OK ] AbstractOptionStorageTest.HandlesTooManyValueAddition (1 ms)
18: [ RUN ] AbstractOptionStorageTest.AllowsEmptyValues
18: [ OK ] AbstractOptionStorageTest.AllowsEmptyValues (1 ms)
18: [----------] 5 tests from AbstractOptionStorageTest (4 ms total)
18:
18: [----------] 8 tests from FileNameOptionTest
18: [ RUN ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredOptionWithoutValue
18: [ OK ] FileNameOptionTest.HandlesRequiredOptionWithoutValue (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalUnsetOption
18: [ OK ] FileNameOptionTest.HandlesOptionalUnsetOption (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalDefaultValueWithoutExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesRequiredCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension
18: [ OK ] FileNameOptionTest.HandlesOptionalCustomDefaultExtension (0 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnUnknownFileSuffix (1 ms)
18: [ RUN ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix
18: [ OK ] FileNameOptionTest.GivesErrorOnInvalidFileSuffix (0 ms)
18: [----------] 8 tests from FileNameOptionTest (1 ms total)
18:
18: [----------] 15 tests from FileNameOptionManagerTest
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtension (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension
18: [ OK ] FileNameOptionManagerTest.AddsMissingCustomDefaultExtension (1 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingGenericInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingDefaultInputFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile
18: [ OK ] FileNameOptionManagerTest.GivesErrorOnMissingRequiredInputFile (1 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingDefaultInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified
18: [ OK ] FileNameOptionManagerTest.AcceptsMissingRequiredInputFileIfSpecified (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalDefaultNameBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForRequiredFromDefaultNameOptionBasedOnExistingFile (0 ms)
18: [ RUN ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile
18: [ OK ] FileNameOptionManagerTest.AddsMissingExtensionForOptionalFromDefaultNameOptionBasedOnExistingFile (1 ms)
18: [ RUN ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking
18: [ OK ] FileNameOptionManagerTest.DefaultNameOptionWorksWithoutInputChecking (0 ms)
18: [----------] 15 tests from FileNameOptionManagerTest (3 ms total)
18:
18: [----------] 1 test from OptionsTest
18: [ RUN ] OptionsTest.FailsOnNonsafeStorage
18: [ OK ] OptionsTest.FailsOnNonsafeStorage (0 ms)
18: [----------] 1 test from OptionsTest (0 ms total)
18:
18: [----------] 9 tests from OptionsAssignerTest
18: [ RUN ] OptionsAssignerTest.HandlesMissingRequiredParameter
18: [ OK ] OptionsAssignerTest.HandlesMissingRequiredParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue
18: [ OK ] OptionsAssignerTest.HandlesRequiredParameterWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesInvalidMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesInvalidMultipleParameter (1 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleParameter
18: [ OK ] OptionsAssignerTest.HandlesMultipleParameter (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMissingValue
18: [ OK ] OptionsAssignerTest.HandlesMissingValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesExtraValue
18: [ OK ] OptionsAssignerTest.HandlesExtraValue (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesGroups
18: [ OK ] OptionsAssignerTest.HandlesGroups (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesSections
18: [ OK ] OptionsAssignerTest.HandlesSections (0 ms)
18: [ RUN ] OptionsAssignerTest.HandlesMultipleSources
18: [ OK ] OptionsAssignerTest.HandlesMultipleSources (0 ms)
18: [----------] 9 tests from OptionsAssignerTest (1 ms total)
18:
18: [----------] 4 tests from OptionsAssignerBooleanTest
18: [ RUN ] OptionsAssignerBooleanTest.StoresYesValue
18: [ OK ] OptionsAssignerBooleanTest.StoresYesValue (1 ms)
18: [ RUN ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue
18: [ OK ] OptionsAssignerBooleanTest.SetsBooleanWithoutExplicitValue (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo
18: [ OK ] OptionsAssignerBooleanTest.ClearsBooleanWithPrefixNo (0 ms)
18: [ RUN ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue
18: [ OK ] OptionsAssignerBooleanTest.HandlesBooleanWithPrefixAndValue (0 ms)
18: [----------] 4 tests from OptionsAssignerBooleanTest (1 ms total)
18:
18: [----------] 13 tests from OptionsAssignerIntegerTest
18: [ RUN ] OptionsAssignerIntegerTest.StoresSingleValue
18: [ OK ] OptionsAssignerIntegerTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesInvalidValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesInvalidValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesOverflow
18: [ OK ] OptionsAssignerIntegerTest.HandlesOverflow (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet
18: [ OK ] OptionsAssignerIntegerTest.StoresDefaultValueIfSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet
18: [ OK ] OptionsAssignerIntegerTest.HandlesDefaultValueIfSetWhenNotSet (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesBothDefaultValues
18: [ OK ] OptionsAssignerIntegerTest.HandlesBothDefaultValues (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.StoresToVector
18: [ OK ] OptionsAssignerIntegerTest.StoresToVector (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectors
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectors (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorFromSingleValue (1 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment
18: [ OK ] OptionsAssignerIntegerTest.HandlesVectorsWithDefaultValueWithInvalidAssignment (0 ms)
18: [----------] 13 tests from OptionsAssignerIntegerTest (2 ms total)
18:
18: [----------] 5 tests from OptionsAssignerDoubleTest
18: [ RUN ] OptionsAssignerDoubleTest.StoresSingleValue
18: [ OK ] OptionsAssignerDoubleTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.StoresValueFromFloat
18: [ OK ] OptionsAssignerDoubleTest.StoresValueFromFloat (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesEmptyValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesEmptyValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPreSetScaleValue (0 ms)
18: [ RUN ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue
18: [ OK ] OptionsAssignerDoubleTest.HandlesPostSetScaleValue (0 ms)
18: [----------] 5 tests from OptionsAssignerDoubleTest (1 ms total)
18:
18: [----------] 9 tests from OptionsAssignerStringTest
18: [ RUN ] OptionsAssignerStringTest.StoresSingleValue
18: [ OK ] OptionsAssignerStringTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray
18: [ OK ] OptionsAssignerStringTest.HandlesEnumValueFromNullTerminatedArray (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesIncorrectEnumValue
18: [ OK ] OptionsAssignerStringTest.HandlesIncorrectEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.CompletesEnumValue
18: [ OK ] OptionsAssignerStringTest.CompletesEnumValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumWithNoValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumWithNoValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerStringTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 9 tests from OptionsAssignerStringTest (1 ms total)
18:
18: [----------] 6 tests from OptionsAssignerEnumTest
18: [ RUN ] OptionsAssignerEnumTest.StoresSingleValue
18: [ OK ] OptionsAssignerEnumTest.StoresSingleValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.StoresVectorValues
18: [ OK ] OptionsAssignerEnumTest.StoresVectorValues (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange
18: [ OK ] OptionsAssignerEnumTest.HandlesInitialValueOutOfRange (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValue
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValue (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVariable (0 ms)
18: [ RUN ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector
18: [ OK ] OptionsAssignerEnumTest.HandlesEnumDefaultValueFromVector (0 ms)
18: [----------] 6 tests from OptionsAssignerEnumTest (0 ms total)
18:
18: [----------] 8 tests from RepeatingOptionSectionTest
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption
18: [ OK ] RepeatingOptionSectionTest.HandlesNoInstanceWithRequiredOption (1 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesSingleInstance
18: [ OK ] RepeatingOptionSectionTest.HandlesSingleInstance (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesDefaultValue
18: [ OK ] RepeatingOptionSectionTest.HandlesDefaultValue (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesTwoInstances
18: [ OK ] RepeatingOptionSectionTest.HandlesTwoInstances (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithImplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault
18: [ OK ] RepeatingOptionSectionTest.HandlesUnsetOptionWithExplicitDefault (0 ms)
18: [ RUN ] RepeatingOptionSectionTest.HandlesNestedSections
18: [ OK ] RepeatingOptionSectionTest.HandlesNestedSections (0 ms)
18: [----------] 8 tests from RepeatingOptionSectionTest (1 ms total)
18:
18: [----------] 1 test from TimeUnitManagerTest
18: [ RUN ] TimeUnitManagerTest.BasicOperations
18: [ OK ] TimeUnitManagerTest.BasicOperations (0 ms)
18: [----------] 1 test from TimeUnitManagerTest (0 ms total)
18:
18: [----------] 4 tests from TimeUnitBehaviorTest
18: [ RUN ] TimeUnitBehaviorTest.ScalesAssignedOptionValue
18: [ OK ] TimeUnitBehaviorTest.ScalesAssignedOptionValue (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues
18: [ OK ] TimeUnitBehaviorTest.DoesNotScaleDefaultValues (1 ms)
18: [ RUN ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources
18: [ OK ] TimeUnitBehaviorTest.ScalesUserInputWithMultipleSources (0 ms)
18: [ RUN ] TimeUnitBehaviorTest.TimeUnitOptionWorks
18: [ OK ] TimeUnitBehaviorTest.TimeUnitOptionWorks (0 ms)
18: [----------] 4 tests from TimeUnitBehaviorTest (1 ms total)
18:
18: [----------] 2 tests from TreeValueSupportAssignTest
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTree
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTree (0 ms)
18: [ RUN ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays
18: [ OK ] TreeValueSupportAssignTest.AssignsFromTreeWithArrays (0 ms)
18: [----------] 2 tests from TreeValueSupportAssignTest (0 ms total)
18:
18: [----------] 1 test from TreeValueSupportAssignErrorTest
18: [ RUN ] TreeValueSupportAssignErrorTest.HandlesInvalidValue
18: [ OK ] TreeValueSupportAssignErrorTest.HandlesInvalidValue (1 ms)
18: [----------] 1 test from TreeValueSupportAssignErrorTest (1 ms total)
18:
18: [----------] 5 tests from TreeValueSupportCheckTest
18: [ RUN ] TreeValueSupportCheckTest.HandlesEmpty
18: [ OK ] TreeValueSupportCheckTest.HandlesEmpty (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesMatchingTree
18: [ OK ] TreeValueSupportCheckTest.HandlesMatchingTree (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree1
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree1 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.HandlesSmallerTree2
18: [ OK ] TreeValueSupportCheckTest.HandlesSmallerTree2 (0 ms)
18: [ RUN ] TreeValueSupportCheckTest.DetectsExtraValue
18: [ OK ] TreeValueSupportCheckTest.DetectsExtraValue (0 ms)
18: [----------] 5 tests from TreeValueSupportCheckTest (0 ms total)
18:
18: [----------] 6 tests from TreeValueSupportAdjustTest
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultValues (1 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultVectorValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultVectorValues (1 ms)
18: [ RUN ] TreeValueSupportAdjustTest.FillsDefaultObjectValues
18: [ OK ] TreeValueSupportAdjustTest.FillsDefaultObjectValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.NormalizesValues
18: [ OK ] TreeValueSupportAdjustTest.NormalizesValues (1 ms)
18: [ RUN ] TreeValueSupportAdjustTest.MergesDefaultValues
18: [ OK ] TreeValueSupportAdjustTest.MergesDefaultValues (0 ms)
18: [ RUN ] TreeValueSupportAdjustTest.OrdersValues
18: [ OK ] TreeValueSupportAdjustTest.OrdersValues (0 ms)
18: [----------] 6 tests from TreeValueSupportAdjustTest (4 ms total)
18:
18: [----------] 8 tests from TreeValueSupportTest
18: [ RUN ] TreeValueSupportTest.SupportsBooleanOption
18: [ OK ] TreeValueSupportTest.SupportsBooleanOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsIntegerOption
18: [ OK ] TreeValueSupportTest.SupportsIntegerOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsInt64Option
18: [ OK ] TreeValueSupportTest.SupportsInt64Option (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsStringOption
18: [ OK ] TreeValueSupportTest.SupportsStringOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsFloatOption
18: [ OK ] TreeValueSupportTest.SupportsFloatOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsDoubleOption
18: [ OK ] TreeValueSupportTest.SupportsDoubleOption (1 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumIntOption
18: [ OK ] TreeValueSupportTest.SupportsEnumIntOption (0 ms)
18: [ RUN ] TreeValueSupportTest.SupportsEnumOption
18: [ OK ] TreeValueSupportTest.SupportsEnumOption (1 ms)
18: [----------] 8 tests from TreeValueSupportTest (5 ms total)
18:
18: [----------] Global test environment tear-down
18: [==========] 110 tests from 18 test cases ran. (26 ms total)
18: [ PASSED ] 110 tests.
18/54 Test #18: OptionsUnitTests .................... Passed 0.10 sec
test 19
Start 19: PbcutilUnitTest
19: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pbcutil-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PbcutilUnitTest.xml"
19: Test timeout computed to be: 30
19: [==========] Running 3 tests from 2 test cases.
19: [----------] Global test environment set-up.
19: [----------] 1 test from PbcTest
19: [ RUN ] PbcTest.CalcShiftsWorks
19: [ OK ] PbcTest.CalcShiftsWorks (3 ms)
19: [----------] 1 test from PbcTest (4 ms total)
19:
19: [----------] 2 tests from PbcEnumsTest
19: [ RUN ] PbcEnumsTest.CenteringTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.CenteringTypeNamesAreCorrect (0 ms)
19: [ RUN ] PbcEnumsTest.UnitCellTypeNamesAreCorrect
19: [ OK ] PbcEnumsTest.UnitCellTypeNamesAreCorrect (0 ms)
19: [----------] 2 tests from PbcEnumsTest (0 ms total)
19:
19: [----------] Global test environment tear-down
19: [==========] 3 tests from 2 test cases ran. (5 ms total)
19: [ PASSED ] 3 tests.
19/54 Test #19: PbcutilUnitTest ..................... Passed 0.07 sec
test 20
Start 20: RandomUnitTests
20: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/random-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RandomUnitTests.xml"
20: Test timeout computed to be: 30
20: [==========] Running 44 tests from 10 test cases.
20: [----------] Global test environment set-up.
20: [----------] 4 tests from ExponentialDistributionTest
20: [ RUN ] ExponentialDistributionTest.Output
20: [ OK ] ExponentialDistributionTest.Output (1 ms)
20: [ RUN ] ExponentialDistributionTest.Logical
20: [ OK ] ExponentialDistributionTest.Logical (0 ms)
20: [ RUN ] ExponentialDistributionTest.Reset
20: [ OK ] ExponentialDistributionTest.Reset (0 ms)
20: [ RUN ] ExponentialDistributionTest.AltParam
20: [ OK ] ExponentialDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from ExponentialDistributionTest (1 ms total)
20:
20: [----------] 4 tests from GammaDistributionTest
20: [ RUN ] GammaDistributionTest.Output
20: [ OK ] GammaDistributionTest.Output (1 ms)
20: [ RUN ] GammaDistributionTest.Logical
20: [ OK ] GammaDistributionTest.Logical (0 ms)
20: [ RUN ] GammaDistributionTest.Reset
20: [ OK ] GammaDistributionTest.Reset (0 ms)
20: [ RUN ] GammaDistributionTest.AltParam
20: [ OK ] GammaDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from GammaDistributionTest (1 ms total)
20:
20: [----------] 4 tests from NormalDistributionTest
20: [ RUN ] NormalDistributionTest.Output
20: [ OK ] NormalDistributionTest.Output (0 ms)
20: [ RUN ] NormalDistributionTest.Logical
20: [ OK ] NormalDistributionTest.Logical (0 ms)
20: [ RUN ] NormalDistributionTest.Reset
20: [ OK ] NormalDistributionTest.Reset (0 ms)
20: [ RUN ] NormalDistributionTest.AltParam
20: [ OK ] NormalDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from NormalDistributionTest (1 ms total)
20:
20: [----------] 1 test from SeedTest
20: [ RUN ] SeedTest.makeRandomSeed
20: [ OK ] SeedTest.makeRandomSeed (29 ms)
20: [----------] 1 test from SeedTest (29 ms total)
20:
20: [----------] 6 tests from TabulatedNormalDistributionTest
20: [ RUN ] TabulatedNormalDistributionTest.Output14
20: [ OK ] TabulatedNormalDistributionTest.Output14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Output16
20: [ OK ] TabulatedNormalDistributionTest.Output16 (1 ms)
20: [ RUN ] TabulatedNormalDistributionTest.OutputDouble14
20: [ OK ] TabulatedNormalDistributionTest.OutputDouble14 (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Logical
20: [ OK ] TabulatedNormalDistributionTest.Logical (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.Reset
20: [ OK ] TabulatedNormalDistributionTest.Reset (0 ms)
20: [ RUN ] TabulatedNormalDistributionTest.AltParam
20: [ OK ] TabulatedNormalDistributionTest.AltParam (0 ms)
20: [----------] 6 tests from TabulatedNormalDistributionTest (2 ms total)
20:
20: [----------] 1 test from TabulatedNormalDistributionTableTest
20: [ RUN ] TabulatedNormalDistributionTableTest.HasValidProperties
20: [ OK ] TabulatedNormalDistributionTableTest.HasValidProperties (8 ms)
20: [----------] 1 test from TabulatedNormalDistributionTableTest (8 ms total)
20:
20: [----------] 6 tests from ThreeFry2x64Test
20: [ RUN ] ThreeFry2x64Test.Logical
20: [ OK ] ThreeFry2x64Test.Logical (0 ms)
20: [ RUN ] ThreeFry2x64Test.InternalCounterSequence
20: [ OK ] ThreeFry2x64Test.InternalCounterSequence (1 ms)
20: [ RUN ] ThreeFry2x64Test.Reseed
20: [ OK ] ThreeFry2x64Test.Reseed (0 ms)
20: [ RUN ] ThreeFry2x64Test.Discard
20: [ OK ] ThreeFry2x64Test.Discard (0 ms)
20: [ RUN ] ThreeFry2x64Test.InvalidCounter
20: [ OK ] ThreeFry2x64Test.InvalidCounter (0 ms)
20: [ RUN ] ThreeFry2x64Test.ExhaustInternalCounter
20: [ OK ] ThreeFry2x64Test.ExhaustInternalCounter (0 ms)
20: [----------] 6 tests from ThreeFry2x64Test (1 ms total)
20:
20: [----------] 4 tests from UniformIntDistributionTest
20: [ RUN ] UniformIntDistributionTest.Output
20: [ OK ] UniformIntDistributionTest.Output (0 ms)
20: [ RUN ] UniformIntDistributionTest.Logical
20: [ OK ] UniformIntDistributionTest.Logical (0 ms)
20: [ RUN ] UniformIntDistributionTest.Reset
20: [ OK ] UniformIntDistributionTest.Reset (0 ms)
20: [ RUN ] UniformIntDistributionTest.AltParam
20: [ OK ] UniformIntDistributionTest.AltParam (0 ms)
20: [----------] 4 tests from UniformIntDistributionTest (0 ms total)
20:
20: [----------] 5 tests from UniformRealDistributionTest
20: [ RUN ] UniformRealDistributionTest.GenerateCanonical
20: [ OK ] UniformRealDistributionTest.GenerateCanonical (1 ms)
20: [ RUN ] UniformRealDistributionTest.Output
20: [ OK ] UniformRealDistributionTest.Output (0 ms)
20: [ RUN ] UniformRealDistributionTest.Logical
20: [ OK ] UniformRealDistributionTest.Logical (0 ms)
20: [ RUN ] UniformRealDistributionTest.Reset
20: [ OK ] UniformRealDistributionTest.Reset (0 ms)
20: [ RUN ] UniformRealDistributionTest.AltParam
20: [ OK ] UniformRealDistributionTest.AltParam (0 ms)
20: [----------] 5 tests from UniformRealDistributionTest (2 ms total)
20:
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/1 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Default/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Default/2 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/1 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Fast/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Fast/2 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/0 (0 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/1 (1 ms)
20: [ RUN ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2
20: [ OK ] KnownAnswersTest/ThreeFry2x64Test.Using40Rounds/2 (0 ms)
20: [----------] 9 tests from KnownAnswersTest/ThreeFry2x64Test (3 ms total)
20:
20: [----------] Global test environment tear-down
20: [==========] 44 tests from 10 test cases ran. (50 ms total)
20: [ PASSED ] 44 tests.
20/54 Test #20: RandomUnitTests ..................... Passed 0.15 sec
test 21
Start 21: RestraintTests
21: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/restraintpotential-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/RestraintTests.xml"
21: Test timeout computed to be: 30
21: [==========] Running 1 test from 1 test case.
21: [----------] Global test environment set-up.
21: [----------] 1 test from RestraintManager
21: [ RUN ] RestraintManager.restraintList
21: [ OK ] RestraintManager.restraintList (0 ms)
21: [----------] 1 test from RestraintManager (0 ms total)
21:
21: [----------] Global test environment tear-down
21: [==========] 1 test from 1 test case ran. (0 ms total)
21: [ PASSED ] 1 test.
21/54 Test #21: RestraintTests ...................... Passed 0.06 sec
test 22
Start 22: TableUnitTests
22: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/table-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TableUnitTests.xml"
22: Test timeout computed to be: 30
22: [==========] Running 16 tests from 2 test cases.
22: [----------] Global test environment set-up.
22: [----------] 8 tests from SplineTableTest/0, where TypeParam = gmx::QuadraticSplineTable
22: [ RUN ] SplineTableTest/0.HandlesIncorrectInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectInput (8 ms)
22: [ RUN ] SplineTableTest/0.Sinc
22: [ OK ] SplineTableTest/0.Sinc (5 ms)
22: [ RUN ] SplineTableTest/0.LJ12
22: [ OK ] SplineTableTest/0.LJ12 (91 ms)
22: [ RUN ] SplineTableTest/0.PmeCorrection
22: [ OK ] SplineTableTest/0.PmeCorrection (8 ms)
22: [ RUN ] SplineTableTest/0.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/0.HandlesIncorrectNumericalInput (2 ms)
22: [ RUN ] SplineTableTest/0.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/0.NumericalInputPmeCorr (7 ms)
22: [ RUN ] SplineTableTest/0.TwoFunctions
22: [ OK ] SplineTableTest/0.TwoFunctions (181 ms)
22: [ RUN ] SplineTableTest/0.ThreeFunctions
22: [ OK ] SplineTableTest/0.ThreeFunctions (275 ms)
22: [----------] 8 tests from SplineTableTest/0 (580 ms total)
22:
22: [----------] 8 tests from SplineTableTest/1, where TypeParam = gmx::CubicSplineTable
22: [ RUN ] SplineTableTest/1.HandlesIncorrectInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectInput (22 ms)
22: [ RUN ] SplineTableTest/1.Sinc
22: [ OK ] SplineTableTest/1.Sinc (9 ms)
22: [ RUN ] SplineTableTest/1.LJ12
22: [ OK ] SplineTableTest/1.LJ12 (251 ms)
22: [ RUN ] SplineTableTest/1.PmeCorrection
22: [ OK ] SplineTableTest/1.PmeCorrection (8 ms)
22: [ RUN ] SplineTableTest/1.HandlesIncorrectNumericalInput
22: [ OK ] SplineTableTest/1.HandlesIncorrectNumericalInput (2 ms)
22: [ RUN ] SplineTableTest/1.NumericalInputPmeCorr
22: [ OK ] SplineTableTest/1.NumericalInputPmeCorr (5 ms)
22: [ RUN ] SplineTableTest/1.TwoFunctions
22: [ OK ] SplineTableTest/1.TwoFunctions (451 ms)
22: [ RUN ] SplineTableTest/1.ThreeFunctions
22: [ OK ] SplineTableTest/1.ThreeFunctions (591 ms)
22: [----------] 8 tests from SplineTableTest/1 (1340 ms total)
22:
22: [----------] Global test environment tear-down
22: [==========] 16 tests from 2 test cases ran. (1921 ms total)
22: [ PASSED ] 16 tests.
22/54 Test #22: TableUnitTests ...................... Passed 1.99 sec
test 23
Start 23: TaskAssignmentUnitTests
23: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/taskassignment-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TaskAssignmentUnitTests.xml"
23: Test timeout computed to be: 30
23: [==========] Running 3 tests from 2 test cases.
23: [----------] Global test environment set-up.
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest
23: [ RUN ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork
23: [ OK ] UserTaskAssignmentStringHandlingTest.ParsingAndReconstructionWork (1 ms)
23: [ RUN ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid
23: [ OK ] UserTaskAssignmentStringHandlingTest.EmptyStringCanBeValid (0 ms)
23: [----------] 2 tests from UserTaskAssignmentStringHandlingTest (1 ms total)
23:
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest
23: [ RUN ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow
23: [ OK ] GpuIdAndAssignmentStringHandlingTest.InvalidInputsThrow (2 ms)
23: [----------] 1 test from GpuIdAndAssignmentStringHandlingTest (2 ms total)
23:
23: [----------] Global test environment tear-down
23: [==========] 3 tests from 2 test cases ran. (4 ms total)
23: [ PASSED ] 3 tests.
23/54 Test #23: TaskAssignmentUnitTests ............. Passed 0.07 sec
test 24
Start 24: TopologyTest
24: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/topology-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TopologyTest.xml"
24: Test timeout computed to be: 30
24: [==========] Running 11 tests from 3 test cases.
24: [----------] Global test environment set-up.
24: [----------] 3 tests from ExclusionBlockTest
24: [ RUN ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks
24: [ OK ] ExclusionBlockTest.ConvertBlockAToExclusionBlocks (0 ms)
24: [ RUN ] ExclusionBlockTest.ConvertExclusionBlockToBlocka
24: [ OK ] ExclusionBlockTest.ConvertExclusionBlockToBlocka (0 ms)
24: [ RUN ] ExclusionBlockTest.MergeExclusions
24: [ OK ] ExclusionBlockTest.MergeExclusions (0 ms)
24: [----------] 3 tests from ExclusionBlockTest (0 ms total)
24:
24: [----------] 2 tests from MtopTest
24: [ RUN ] MtopTest.RangeBasedLoop
24: [ OK ] MtopTest.RangeBasedLoop (0 ms)
24: [ RUN ] MtopTest.Operators
24: [ OK ] MtopTest.Operators (1 ms)
24: [----------] 2 tests from MtopTest (1 ms total)
24:
24: [----------] 6 tests from SymtabTest
24: [ RUN ] SymtabTest.EmptyOnOpen
24: [ OK ] SymtabTest.EmptyOnOpen (0 ms)
24: [ RUN ] SymtabTest.AddSingleEntry
24: [ OK ] SymtabTest.AddSingleEntry (0 ms)
24: [ RUN ] SymtabTest.AddTwoDistinctEntries
24: [ OK ] SymtabTest.AddTwoDistinctEntries (0 ms)
24: [ RUN ] SymtabTest.TryToAddDuplicates
24: [ OK ] SymtabTest.TryToAddDuplicates (0 ms)
24: [ RUN ] SymtabTest.AddLargeNumberOfEntries
24: [ OK ] SymtabTest.AddLargeNumberOfEntries (1 ms)
24: [ RUN ] SymtabTest.NoDuplicatesInLargeTable
24: [ OK ] SymtabTest.NoDuplicatesInLargeTable (1 ms)
24: [----------] 6 tests from SymtabTest (2 ms total)
24:
24: [----------] Global test environment tear-down
24: [==========] 11 tests from 3 test cases ran. (4 ms total)
24: [ PASSED ] 11 tests.
24/54 Test #24: TopologyTest ........................ Passed 0.09 sec
test 25
Start 25: PullTest
25: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pull-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/PullTest.xml"
25: Test timeout computed to be: 30
25: [==========] Running 5 tests from 1 test case.
25: [----------] Global test environment set-up.
25: [----------] 5 tests from PullTest
25: [ RUN ] PullTest.MaxPullDistanceXyzScrewBox
25: [ OK ] PullTest.MaxPullDistanceXyzScrewBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzCubicBox
25: [ OK ] PullTest.MaxPullDistanceXyzCubicBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzTricBox
25: [ OK ] PullTest.MaxPullDistanceXyzTricBox (1 ms)
25: [ RUN ] PullTest.MaxPullDistanceXyzLongBox
25: [ OK ] PullTest.MaxPullDistanceXyzLongBox (0 ms)
25: [ RUN ] PullTest.MaxPullDistanceXySkewedBox
25: [ OK ] PullTest.MaxPullDistanceXySkewedBox (0 ms)
25: [----------] 5 tests from PullTest (1 ms total)
25:
25: [----------] Global test environment tear-down
25: [==========] 5 tests from 1 test case ran. (2 ms total)
25: [ PASSED ] 5 tests.
25/54 Test #25: PullTest ............................ Passed 0.06 sec
test 26
Start 26: AwhTest
26: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/awh-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AwhTest.xml"
26: Test timeout computed to be: 30
26: [==========] Running 12 tests from 4 test cases.
26: [----------] Global test environment set-up.
26: [----------] 1 test from BiasTest
26: [ RUN ] BiasTest.DetectsCovering
26: [ OK ] BiasTest.DetectsCovering (3 ms)
26: [----------] 1 test from BiasTest (3 ms total)
26:
26: [----------] 1 test from gridTest
26: [ RUN ] gridTest.neighborhood
26: [ OK ] gridTest.neighborhood (10 ms)
26: [----------] 1 test from gridTest (10 ms total)
26:
26: [----------] 8 tests from WithParameters/BiasTest
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/0
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/0 (2 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/1
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/1 (3 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/2
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/2 (2 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/3
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/3 (3 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/4
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/4 (2 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/5
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/5 (2 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/6
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/6 (2 ms)
26: [ RUN ] WithParameters/BiasTest.ForcesBiasPmf/7
26: [ OK ] WithParameters/BiasTest.ForcesBiasPmf/7 (2 ms)
26: [----------] 8 tests from WithParameters/BiasTest (20 ms total)
26:
26: [----------] 2 tests from WithParameters/BiasStateTest
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/0
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/0 (1 ms)
26: [ RUN ] WithParameters/BiasStateTest.InitializesFromFile/1
26: [ OK ] WithParameters/BiasStateTest.InitializesFromFile/1 (1 ms)
26: [----------] 2 tests from WithParameters/BiasStateTest (3 ms total)
26:
26: [----------] Global test environment tear-down
26: [==========] 12 tests from 4 test cases ran. (36 ms total)
26: [ PASSED ] 12 tests.
26/54 Test #26: AwhTest ............................. Passed 0.10 sec
test 27
Start 27: SimdUnitTests
27: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/simd-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SimdUnitTests.xml"
27: Test timeout computed to be: 30
27: [==========] Running 86 tests from 3 test cases.
27: [----------] Global test environment set-up.
27: [----------] 41 tests from SimdScalarTest
27: [ RUN ] SimdScalarTest.load
27: [ OK ] SimdScalarTest.load (0 ms)
27: [ RUN ] SimdScalarTest.loadU
27: [ OK ] SimdScalarTest.loadU (0 ms)
27: [ RUN ] SimdScalarTest.store
27: [ OK ] SimdScalarTest.store (0 ms)
27: [ RUN ] SimdScalarTest.storeU
27: [ OK ] SimdScalarTest.storeU (0 ms)
27: [ RUN ] SimdScalarTest.setZero
27: [ OK ] SimdScalarTest.setZero (0 ms)
27: [ RUN ] SimdScalarTest.andNot
27: [ OK ] SimdScalarTest.andNot (0 ms)
27: [ RUN ] SimdScalarTest.fma
27: [ OK ] SimdScalarTest.fma (0 ms)
27: [ RUN ] SimdScalarTest.fms
27: [ OK ] SimdScalarTest.fms (0 ms)
27: [ RUN ] SimdScalarTest.fnma
27: [ OK ] SimdScalarTest.fnma (0 ms)
27: [ RUN ] SimdScalarTest.fnms
27: [ OK ] SimdScalarTest.fnms (1 ms)
27: [ RUN ] SimdScalarTest.maskAdd
27: [ OK ] SimdScalarTest.maskAdd (0 ms)
27: [ RUN ] SimdScalarTest.maskzMul
27: [ OK ] SimdScalarTest.maskzMul (0 ms)
27: [ RUN ] SimdScalarTest.maskzFma
27: [ OK ] SimdScalarTest.maskzFma (0 ms)
27: [ RUN ] SimdScalarTest.abs
27: [ OK ] SimdScalarTest.abs (0 ms)
27: [ RUN ] SimdScalarTest.max
27: [ OK ] SimdScalarTest.max (0 ms)
27: [ RUN ] SimdScalarTest.min
27: [ OK ] SimdScalarTest.min (0 ms)
27: [ RUN ] SimdScalarTest.round
27: [ OK ] SimdScalarTest.round (0 ms)
27: [ RUN ] SimdScalarTest.trunc
27: [ OK ] SimdScalarTest.trunc (0 ms)
27: [ RUN ] SimdScalarTest.reduce
27: [ OK ] SimdScalarTest.reduce (0 ms)
27: [ RUN ] SimdScalarTest.testBits
27: [ OK ] SimdScalarTest.testBits (0 ms)
27: [ RUN ] SimdScalarTest.anyTrue
27: [ OK ] SimdScalarTest.anyTrue (0 ms)
27: [ RUN ] SimdScalarTest.selectByMask
27: [ OK ] SimdScalarTest.selectByMask (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMask
27: [ OK ] SimdScalarTest.selectByNotMask (1 ms)
27: [ RUN ] SimdScalarTest.blend
27: [ OK ] SimdScalarTest.blend (0 ms)
27: [ RUN ] SimdScalarTest.cvtR2I
27: [ OK ] SimdScalarTest.cvtR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvttR2I
27: [ OK ] SimdScalarTest.cvttR2I (0 ms)
27: [ RUN ] SimdScalarTest.cvtI2R
27: [ OK ] SimdScalarTest.cvtI2R (1 ms)
27: [ RUN ] SimdScalarTest.cvtF2D
27: [ OK ] SimdScalarTest.cvtF2D (0 ms)
27: [ RUN ] SimdScalarTest.cvtD2D
27: [ OK ] SimdScalarTest.cvtD2D (0 ms)
27: [ RUN ] SimdScalarTest.loadI
27: [ OK ] SimdScalarTest.loadI (0 ms)
27: [ RUN ] SimdScalarTest.loadUI
27: [ OK ] SimdScalarTest.loadUI (0 ms)
27: [ RUN ] SimdScalarTest.storeI
27: [ OK ] SimdScalarTest.storeI (0 ms)
27: [ RUN ] SimdScalarTest.storeUI
27: [ OK ] SimdScalarTest.storeUI (0 ms)
27: [ RUN ] SimdScalarTest.andNotI
27: [ OK ] SimdScalarTest.andNotI (0 ms)
27: [ RUN ] SimdScalarTest.testBitsI
27: [ OK ] SimdScalarTest.testBitsI (0 ms)
27: [ RUN ] SimdScalarTest.selectByMaskI
27: [ OK ] SimdScalarTest.selectByMaskI (0 ms)
27: [ RUN ] SimdScalarTest.selectByNotMaskI
27: [ OK ] SimdScalarTest.selectByNotMaskI (0 ms)
27: [ RUN ] SimdScalarTest.blendI
27: [ OK ] SimdScalarTest.blendI (0 ms)
27: [ RUN ] SimdScalarTest.cvtB2IB
27: [ OK ] SimdScalarTest.cvtB2IB (0 ms)
27: [ RUN ] SimdScalarTest.cvtIB2B
27: [ OK ] SimdScalarTest.cvtIB2B (0 ms)
27: [ RUN ] SimdScalarTest.expandScalarsToTriplets
27: [ OK ] SimdScalarTest.expandScalarsToTriplets (0 ms)
27: [----------] 41 tests from SimdScalarTest (10 ms total)
27:
27: [----------] 8 tests from SimdScalarUtilTest
27: [ RUN ] SimdScalarUtilTest.gatherLoadTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterStoreU
27: [ OK ] SimdScalarUtilTest.transposeScatterStoreU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterIncrU
27: [ OK ] SimdScalarUtilTest.transposeScatterIncrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.transposeScatterDecrU
27: [ OK ] SimdScalarUtilTest.transposeScatterDecrU (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose
27: [ OK ] SimdScalarUtilTest.gatherLoadUBySimdIntTranspose (0 ms)
27: [ RUN ] SimdScalarUtilTest.reduceIncr4ReturnSum
27: [ OK ] SimdScalarUtilTest.reduceIncr4ReturnSum (0 ms)
27: [----------] 8 tests from SimdScalarUtilTest (2 ms total)
27:
27: [----------] 37 tests from SimdScalarMathTest
27: [ RUN ] SimdScalarMathTest.copysign
27: [ OK ] SimdScalarMathTest.copysign (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPair
27: [ OK ] SimdScalarMathTest.invsqrtPair (0 ms)
27: [ RUN ] SimdScalarMathTest.inv
27: [ OK ] SimdScalarMathTest.inv (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrt
27: [ OK ] SimdScalarMathTest.maskzInvsqrt (0 ms)
27: [ RUN ] SimdScalarMathTest.log
27: [ OK ] SimdScalarMathTest.log (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2
27: [ OK ] SimdScalarMathTest.exp2 (0 ms)
27: [ RUN ] SimdScalarMathTest.exp
27: [ OK ] SimdScalarMathTest.exp (0 ms)
27: [ RUN ] SimdScalarMathTest.erf
27: [ OK ] SimdScalarMathTest.erf (0 ms)
27: [ RUN ] SimdScalarMathTest.erfc
27: [ OK ] SimdScalarMathTest.erfc (0 ms)
27: [ RUN ] SimdScalarMathTest.sincos
27: [ OK ] SimdScalarMathTest.sincos (0 ms)
27: [ RUN ] SimdScalarMathTest.sin
27: [ OK ] SimdScalarMathTest.sin (0 ms)
27: [ RUN ] SimdScalarMathTest.cos
27: [ OK ] SimdScalarMathTest.cos (0 ms)
27: [ RUN ] SimdScalarMathTest.tan
27: [ OK ] SimdScalarMathTest.tan (0 ms)
27: [ RUN ] SimdScalarMathTest.asin
27: [ OK ] SimdScalarMathTest.asin (0 ms)
27: [ RUN ] SimdScalarMathTest.acos
27: [ OK ] SimdScalarMathTest.acos (0 ms)
27: [ RUN ] SimdScalarMathTest.atan
27: [ OK ] SimdScalarMathTest.atan (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2
27: [ OK ] SimdScalarMathTest.atan2 (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrection
27: [ OK ] SimdScalarMathTest.pmeForceCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrection
27: [ OK ] SimdScalarMathTest.pmePotentialCorrection (0 ms)
27: [ RUN ] SimdScalarMathTest.invsqrtPairSingleAccuracy
27: [ OK ] SimdScalarMathTest.invsqrtPairSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.invSingleAccuracy
27: [ OK ] SimdScalarMathTest.invSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy
27: [ OK ] SimdScalarMathTest.maskzInvsqrtSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.logSingleAccuracy
27: [ OK ] SimdScalarMathTest.logSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.exp2SingleAccuracy
27: [ OK ] SimdScalarMathTest.exp2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.expSingleAccuracy
27: [ OK ] SimdScalarMathTest.expSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.erfcSingleAccuracy
27: [ OK ] SimdScalarMathTest.erfcSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sincosSingleAccuracy
27: [ OK ] SimdScalarMathTest.sincosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.sinSingleAccuracy
27: [ OK ] SimdScalarMathTest.sinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.cosSingleAccuracy
27: [ OK ] SimdScalarMathTest.cosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.tanSingleAccuracy
27: [ OK ] SimdScalarMathTest.tanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.asinSingleAccuracy
27: [ OK ] SimdScalarMathTest.asinSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.acosSingleAccuracy
27: [ OK ] SimdScalarMathTest.acosSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atanSingleAccuracy
27: [ OK ] SimdScalarMathTest.atanSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.atan2SingleAccuracy
27: [ OK ] SimdScalarMathTest.atan2SingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmeForceCorrectionSingleAccuracy (0 ms)
27: [ RUN ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy
27: [ OK ] SimdScalarMathTest.pmePotentialCorrectionSingleAccuracy (0 ms)
27: [----------] 37 tests from SimdScalarMathTest (8 ms total)
27:
27: [----------] Global test environment tear-down
27: [==========] 86 tests from 3 test cases ran. (21 ms total)
27: [ PASSED ] 86 tests.
27/54 Test #27: SimdUnitTests ....................... Passed 0.09 sec
test 28
Start 28: CompatibilityHelpersTests
28: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/compat-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CompatibilityHelpersTests.xml"
28: Test timeout computed to be: 30
28: [==========] Running 170 tests from 12 test cases.
28: [----------] Global test environment set-up.
28: [----------] 45 tests from OptionalTest
28: [ RUN ] OptionalTest.UnionCanContainNonPodTypes
28: [ OK ] OptionalTest.UnionCanContainNonPodTypes (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructEmpty
28: [ OK ] OptionalTest.CanDefaultConstructEmpty (1 ms)
28: [ RUN ] OptionalTest.CanConstructFromNullopt
28: [ OK ] OptionalTest.CanConstructFromNullopt (0 ms)
28: [ RUN ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType
28: [ OK ] OptionalTest.CanDefaultConstructUsingNonDefaultConstructibleType (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalWithExplicitConversion (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanCopyConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptional
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptional (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromNonEmptyOptionalNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteral
28: [ OK ] OptionalTest.CanCopyConstructFromLiteral (1 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromLiteralConverting
28: [ OK ] OptionalTest.CanCopyConstructFromLiteralConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValue
28: [ OK ] OptionalTest.CanCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyConstructFromValueConverting
28: [ OK ] OptionalTest.CanCopyConstructFromValueConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValue
28: [ OK ] OptionalTest.CanMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting
28: [ OK ] OptionalTest.CanMoveConstructFromValueNonExplicitConverting (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceConstructFromLiteral
28: [ OK ] OptionalTest.CanInPlaceConstructFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromValue
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromValue (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceCopyConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceCopyConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanInPlaceMoveConstructFromInitializerList
28: [ OK ] OptionalTest.CanInPlaceMoveConstructFromInitializerList (0 ms)
28: [ RUN ] OptionalTest.CanAssignNulloptToDisengage
28: [ OK ] OptionalTest.CanAssignNulloptToDisengage (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanCopyAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting
28: [ OK ] OptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionalsConverting (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromLiteral
28: [ OK ] OptionalTest.CanCopyAssignFromLiteral (0 ms)
28: [ RUN ] OptionalTest.CanCopyAssignFromValue
28: [ OK ] OptionalTest.CanCopyAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanMoveAssignFromValue
28: [ OK ] OptionalTest.CanMoveAssignFromValue (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromArguments (0 ms)
28: [ RUN ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanCopyEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments
28: [ OK ] OptionalTest.CanMoveEmplaceFromInitializerListAndArguments (0 ms)
28: [ RUN ] OptionalTest.CanResetContent
28: [ OK ] OptionalTest.CanResetContent (0 ms)
28: [ RUN ] OptionalTest.ProvidesRelationalOperators
28: [ OK ] OptionalTest.ProvidesRelationalOperators (1 ms)
28: [ RUN ] OptionalTest.ProvidesMixedTypeRelationalOperators
28: [ OK ] OptionalTest.ProvidesMixedTypeRelationalOperators (1 ms)
28: [ RUN ] OptionalTest.CanProduceHash
28: [ OK ] OptionalTest.CanProduceHash (0 ms)
28: [ RUN ] OptionalTest.ShowAlignmentDependingOnBaseType
28: alignment_of<char>: 1
28: alignment_of<short>: 2
28: alignment_of<int>: 4
28: alignment_of<long>: 4
28: alignment_of<float>: 4
28: alignment_of<double>: 8
28: alignment_of<long double>: 8
28: alignment_of<Struct>: 1
28: [ OK ] OptionalTest.ShowAlignmentDependingOnBaseType (0 ms)
28: [ RUN ] OptionalTest.ShowSizeDependingOnBaseType
28: sizeof( nonstd::optional_lite::detail::storage_t<char> ): 1
28: sizeof( optional<char> ): 2 (1)
28: sizeof( optional<short> ): 4 (2)
28: sizeof( optional<int> ): 8 (4)
28: sizeof( optional<long> ): 8 (4)
28: sizeof( optional<float> ): 8 (4)
28: sizeof( optional<double> ): 16 (8)
28: sizeof( optional<long double> ): 16 (8)
28: sizeof( optional<Struct> ): 2 (1)
28: [ OK ] OptionalTest.ShowSizeDependingOnBaseType (0 ms)
28: [----------] 45 tests from OptionalTest (5 ms total)
28:
28: [----------] 7 tests from MakeOptionalTest
28: [ RUN ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals
28: [ OK ] MakeOptionalTest.CanMoveAssignBetweenEngagedAndDisengagedOptionals (0 ms)
28: [ RUN ] MakeOptionalTest.CanCopyConstruct
28: [ OK ] MakeOptionalTest.CanCopyConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanMoveConstruct
28: [ OK ] MakeOptionalTest.CanMoveConstruct (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceCopyConstructFromInitializerListAndArguments (0 ms)
28: [ RUN ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments
28: [ OK ] MakeOptionalTest.CanInPlaceMoveConstructFromInitializerListAndArguments (0 ms)
28: [----------] 7 tests from MakeOptionalTest (1 ms total)
28:
28: [----------] 4 tests from OptionalMemberSwapTest
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithDisengaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapDisengagedWithEngaged (0 ms)
28: [ RUN ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged
28: [ OK ] OptionalMemberSwapTest.CanSwapEngagedWithEngaged (0 ms)
28: [----------] 4 tests from OptionalMemberSwapTest (0 ms total)
28:
28: [----------] 4 tests from OptionalImplicitValueTest
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainValueNonConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueConst (0 ms)
28: [ RUN ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst
28: [ OK ] OptionalImplicitValueTest.CanObtainMovedFromValueNonConst (0 ms)
28: [----------] 4 tests from OptionalImplicitValueTest (0 ms total)
28:
28: [----------] 20 tests from OptionalIntValueTest
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueFromDereferenceOperatorNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool
28: [ OK ] OptionalIntValueTest.CanObtainHasValueViaOperatorBool (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst
28: [ OK ] OptionalIntValueTest.CanObtainMovedValueViaValueMethodNonConst (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainValueFromNonEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainDefaultFromEmptyOptionalViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForLValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod
28: [ OK ] OptionalIntValueTest.CanObtainMovedFromValueForRValuesViaValueOrMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForLValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessAtDisengagedAccessForRValues (0 ms)
28: [ RUN ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod
28: [ OK ] OptionalIntValueTest.ThrowsBadOptionalAccessWithNonEmptyWhatMethod (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithDisengaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapDisengagnedWithEngaged (0 ms)
28: [ RUN ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged
28: [ OK ] OptionalIntValueTest.CanNonMemberSwapEngagnedWithDisengaged (0 ms)
28: [----------] 20 tests from OptionalIntValueTest (2 ms total)
28:
28: [----------] 1 test from NotNullConstruction
28: [ RUN ] NotNullConstruction.Works
28: [ OK ] NotNullConstruction.Works (0 ms)
28: [----------] 1 test from NotNullConstruction (0 ms total)
28:
28: [----------] 1 test from NotNullCasting
28: [ RUN ] NotNullCasting.Works
28: [ OK ] NotNullCasting.Works (0 ms)
28: [----------] 1 test from NotNullCasting (0 ms total)
28:
28: [----------] 1 test from NotNullAssignment
28: [ RUN ] NotNullAssignment.Works
28: [ OK ] NotNullAssignment.Works (0 ms)
28: [----------] 1 test from NotNullAssignment (0 ms total)
28:
28: [----------] 1 test from MakeNotNull
28: [ RUN ] MakeNotNull.Works
28: [ OK ] MakeNotNull.Works (0 ms)
28: [----------] 1 test from MakeNotNull (0 ms total)
28:
28: [----------] 1 test from NotNull
28: [ RUN ] NotNull.WorksInContainers
28: [ OK ] NotNull.WorksInContainers (0 ms)
28: [----------] 1 test from NotNull (0 ms total)
28:
28: [----------] 80 tests from StringViewTest
28: [ RUN ] StringViewTest.CanDefaultConstructEmptyView
28: [ OK ] StringViewTest.CanDefaultConstructEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromPointerAndSize
28: [ OK ] StringViewTest.CanConstructFromPointerAndSize (0 ms)
28: [ RUN ] StringViewTest.CanConstructFromCString
28: [ OK ] StringViewTest.CanConstructFromCString (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyConstructFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyConstructFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromEmptyView (0 ms)
28: [ RUN ] StringViewTest.CanCopyAssingFromNonEmptyView
28: [ OK ] StringViewTest.CanCopyAssingFromNonEmptyView (0 ms)
28: [ RUN ] StringViewTest.AllowForwardIteration
28: [ OK ] StringViewTest.AllowForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowConstForwardIteration
28: [ OK ] StringViewTest.AllowConstForwardIteration (0 ms)
28: [ RUN ] StringViewTest.AllowReverseIteration
28: [ OK ] StringViewTest.AllowReverseIteration (1 ms)
28: [ RUN ] StringViewTest.AllowConstReverseIteration
28: [ OK ] StringViewTest.AllowConstReverseIteration (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaSize
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaSize (0 ms)
28: [ RUN ] StringViewTest.CanObtainSizeFromViewViaLength
28: [ OK ] StringViewTest.CanObtainSizeFromViewViaLength (0 ms)
28: [ RUN ] StringViewTest.CanObtainMaxSizeViaMaxSize
28: [ OK ] StringViewTest.CanObtainMaxSizeViaMaxSize (0 ms)
28: [ RUN ] StringViewTest.CanCheckForEmptyStringWithEmpty
28: [ OK ] StringViewTest.CanCheckForEmptyStringWithEmpty (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaArrayIndex
28: [ OK ] StringViewTest.CanAccessElementViaArrayIndex (0 ms)
28: [ RUN ] StringViewTest.CanAccessElementViaAt
28: [ OK ] StringViewTest.CanAccessElementViaAt (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsAccess
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsAccess (0 ms)
28: [ RUN ] StringViewTest.CanAccessAllElementsViaData
28: [ OK ] StringViewTest.CanAccessAllElementsViaData (0 ms)
28: [ RUN ] StringViewTest.DataFromEmptyStringIsNullptr
28: [ OK ] StringViewTest.DataFromEmptyStringIsNullptr (0 ms)
28: [ RUN ] StringViewTest.CanRemovePrefix
28: [ OK ] StringViewTest.CanRemovePrefix (0 ms)
28: [ RUN ] StringViewTest.CanRemoveSuffix
28: [ OK ] StringViewTest.CanRemoveSuffix (0 ms)
28: [ RUN ] StringViewTest.CanSwapWithOtherView
28: [ OK ] StringViewTest.CanSwapWithOtherView (0 ms)
28: [ RUN ] StringViewTest.CanCopySubstringWithCopy
28: [ OK ] StringViewTest.CanCopySubstringWithCopy (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsCopy
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsCopy (0 ms)
28: [ RUN ] StringViewTest.CanObtainSubstringWithSubstr
28: [ OK ] StringViewTest.CanObtainSubstringWithSubstr (0 ms)
28: [ RUN ] StringViewTest.ThrowsOnOutOfBoundsSubstr
28: [ OK ] StringViewTest.ThrowsOnOutOfBoundsSubstr (0 ms)
28: [ RUN ] StringViewTest.CanLexicallyCompareViewWithCompare
28: [ OK ] StringViewTest.CanLexicallyCompareViewWithCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareEmptyViewsWIthCompare
28: [ OK ] StringViewTest.CanCompareEmptyViewsWIthCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringWithSubStringViewViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare
28: [ OK ] StringViewTest.CanCompareSubStringToCStringPrefixViaCompare (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixViewViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixViewViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCharacterViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForPrefixCStringViaStartsWith
28: [ OK ] StringViewTest.CanCheckForPrefixCStringViaStartsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixViewViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixViewViaEndsWith (1 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCharacterViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanCheckForSuffixCStringViaEndsWith
28: [ OK ] StringViewTest.CanCheckForSuffixCStringViaEndsWith (0 ms)
28: [ RUN ] StringViewTest.CanSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForViewSubstrViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCharacterViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCharacterViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFind (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos
28: [ OK ] StringViewTest.CanBackwardsSearchForCStringSubstringViaFindWithDefaultPos (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharacter
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCStringInLenght (1 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanSearchForFirstOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfAnyCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCStringInLenght (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForLastOccurenceOfCharactersInCString (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNotFoundCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNotFoundCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView
28: [ OK ] StringViewTest.CanBackwardsSearchForForstNonFoundCharacterInView (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonMatchingCharacter (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCStringInLength (0 ms)
28: [ RUN ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString
28: [ OK ] StringViewTest.CanBackwardsSearchForFirstNonEqualToAnyCharacterInCString (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSV
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteralSVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SV
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SV (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInStringViewLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace
28: [ OK ] StringViewTest.CanCreateViewWithLiteral_SVInLiteralsNamespace (0 ms)
28: [ RUN ] StringViewTest.CanCompareToViews
28: [ OK ] StringViewTest.CanCompareToViews (0 ms)
28: [ RUN ] StringViewTest.CanCompareViewToImplicitlyConvertedView
28: [ OK ] StringViewTest.CanCompareViewToImplicitlyConvertedView (0 ms)
28: [ RUN ] StringViewTest.EmptyViewsCompareAsEqual
28: [ OK ] StringViewTest.EmptyViewsCompareAsEqual (0 ms)
28: [ RUN ] StringViewTest.CanPrintViewToPutputStream
28: [ OK ] StringViewTest.CanPrintViewToPutputStream (0 ms)
28: [ RUN ] StringViewTest.HashOfViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfWStringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfWStringViewIsEqualToHashOfString (1 ms)
28: [ RUN ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU16StringViewIsEqualToHashOfString (0 ms)
28: [ RUN ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString
28: [ OK ] StringViewTest.HashOfU32StringViewIsEqualToHashOfString (0 ms)
28: [----------] 80 tests from StringViewTest (6 ms total)
28:
28: [----------] 5 tests from StringViewExtensionTest
28: [ RUN ] StringViewExtensionTest.CanConstructViewFromString
28: [ OK ] StringViewExtensionTest.CanConstructViewFromString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaExplicitOperator (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToString
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToString (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViaToStringFreeFunction (0 ms)
28: [ RUN ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView
28: [ OK ] StringViewExtensionTest.CanConvertViewToStringViewViaToStringView (0 ms)
28: [----------] 5 tests from StringViewExtensionTest (0 ms total)
28:
28: [----------] Global test environment tear-down
28: [==========] 170 tests from 12 test cases ran. (15 ms total)
28: [ PASSED ] 170 tests.
28/54 Test #28: CompatibilityHelpersTests ........... Passed 0.10 sec
test 29
Start 29: GmxAnaTest
29: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxana-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxAnaTest.xml"
29: Test timeout computed to be: 600
29: [==========] Running 27 tests from 5 test cases.
29: [----------] Global test environment set-up.
29: [----------] 5 tests from Entropy
29: [ RUN ] Entropy.Schlitter_300_NoLinear
29: [ OK ] Entropy.Schlitter_300_NoLinear (1 ms)
29: [ RUN ] Entropy.Schlitter_300_Linear
29: [ OK ] Entropy.Schlitter_300_Linear (1 ms)
29: [ RUN ] Entropy.QuasiHarmonic_300_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_300_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_NoLinear
29: [ OK ] Entropy.QuasiHarmonic_200_NoLinear (0 ms)
29: [ RUN ] Entropy.QuasiHarmonic_200_Linear
29: [ OK ] Entropy.QuasiHarmonic_200_Linear (0 ms)
29: [----------] 5 tests from Entropy (3 ms total)
29:
29: [----------] 10 tests from MindistTest
29: [ RUN ] MindistTest.mindistWorksWithSingleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistWorksWithSingleAtoms (7 ms)
29: [ RUN ] MindistTest.mindistWorksWithMultipleAtoms
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.mindistWorksWithMultipleAtoms (5 ms)
29: [ RUN ] MindistTest.mindistDoesNotPickUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistDoesNotPickUpContacts (5 ms)
29: [ RUN ] MindistTest.mindistPicksUpContacts
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.mindistPicksUpContacts (5 ms)
29: [ RUN ] MindistTest.ngWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.ngWorks (4 ms)
29: [ RUN ] MindistTest.groupWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.groupWorks (6 ms)
29: [ RUN ] MindistTest.maxDistWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 2: 'atom3'
29: Selected 3: 'atoms12'
29: [ OK ] MindistTest.maxDistWorks (4 ms)
29: [ RUN ] MindistTest.noPbcWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 0: 'atom1'
29: Selected 1: 'atom2'
29: [ OK ] MindistTest.noPbcWorks (5 ms)
29: [ RUN ] MindistTest.resPerTimeWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 3: 'atoms12'
29: Selected 2: 'atom3'
29: [ OK ] MindistTest.resPerTimeWorks (5 ms)
29: [ RUN ] MindistTest.matrixWorks
29: Group 0 ( atom1) has 1 elements
29: Group 1 ( atom2) has 1 elements
29: Group 2 ( atom3) has 1 elements
29: Group 3 ( atoms12) has 2 elements
29: Group 4 ( atoms23) has 2 elements
29: Group 5 ( atoms123) has 3 elements
29: Select a group: Reading frames from gro file 'mindist_beads', 3 atoms.
29:
Reading frame 0 time 0.000
Last frame 0 time 0.000
29: Selected 5: 'atoms123'
29: Special case: making distance matrix between all atoms in group atoms123
29: [ OK ] MindistTest.matrixWorks (5 ms)
29: [----------] 10 tests from MindistTest (52 ms total)
29:
29: [----------] 3 tests from MsdTest
29: [ RUN ] MsdTest.threeDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 4.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.threeDimensionalDiffusion (5 ms)
29: [ RUN ] MsdTest.twoDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 6.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.twoDimensionalDiffusion (5 ms)
29: [ RUN ] MsdTest.oneDimensionalDiffusion
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( particles) has 3 elements
29: There is one group in the index
29:
Reading frame 0 time 0.000
Reading frame 1 time 1.000
Reading frame 2 time 2.000
Reading frame 3 time 3.000
Reading frame 4 time 4.000
Reading frame 5 time 5.000
Reading frame 6 time 6.000
Reading frame 7 time 7.000
Reading frame 8 time 8.000
Reading frame 9 time 9.000
Last frame 9 time 9.000
29:
29: Used 1 restart points spaced 200 ps over 9 ps
29:
29: Fitting from 1 to 8 ps
29:
29: D[ particles] 8.0000 (+/- 0.0000) 1e-5 cm^2/s
29: [ OK ] MsdTest.oneDimensionalDiffusion (4 ms)
29: [----------] 3 tests from MsdTest (15 ms total)
29:
29: [----------] 3 tests from MsdMolTest
29: [ RUN ] MsdMolTest.diffMolMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -1073743938
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolMassWeighted.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolMassWeighted (4067 ms)
29: [ RUN ] MsdMolTest.diffMolNonMassWeighted
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -1078290897
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolNonMassWeighted.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( water) has 15 elements
29: There is one group in the index
29: Split group of 15 atoms into 5 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 6.4731 Std. Dev. = 8.0969 Error = 3.6210
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ water] 6.5741 (+/- 0.7753) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolNonMassWeighted (4043 ms)
29: [ RUN ] MsdMolTest.diffMolSelected
29:
29: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: For a correct single-point energy evaluation with nsteps = 0, use
29: continuation = yes to avoid constraining the input coordinates.
29:
29: Setting the LD random seed to -50332297
29: Generated 330891 of the 330891 non-bonded parameter combinations
29: Generating 1-4 interactions: fudge = 0.5
29: Generated 330891 of the 330891 1-4 parameter combinations
29: Excluding 2 bonded neighbours molecule type 'SOL'
29: Number of degrees of freedom in T-Coupling group rest is 27.00
29:
29: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: NVE simulation with an initial temperature of zero: will use a Verlet
29: buffer of 10%. Check your energy drift!
29:
29:
29: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.mdp]:
29: You are using a plain Coulomb cut-off, which might produce artifacts.
29: You might want to consider using PME electrostatics.
29:
29:
29:
29: There were 3 notes
29: Calculating diffusion coefficients for molecules.
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
29: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxana/tests/Testing/Temporary/MsdMolTest_diffMolSelected.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
29:
29: Select a group to calculate mean squared displacement for:
29: Group 0 ( mol) has 9 elements
29: There is one group in the index
29: Split group of 9 atoms into 3 molecules
29: Reading frames from pdb file
Reading frame 0 time 0.000 'water t= 0.00400 step= 20', 15 atoms
29:
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Reading frame 5 time 0.020
Reading frame 6 time 0.024
Reading frame 7 time 0.028
Reading frame 8 time 0.032
Reading frame 9 time 0.036
Reading frame 10 time 0.040
Reading frame 11 time 0.044
Reading frame 12 time 0.048
Reading frame 13 time 0.052
Reading frame 14 time 0.056
Reading frame 15 time 0.060
Reading frame 16 time 0.064
Reading frame 17 time 0.068
Reading frame 18 time 0.072
Reading frame 19 time 0.076
Reading frame 20 time 0.080
29:
29: Used 1 restart points spaced 200 ps over 0.1 ps
29:
29: This run will generate roughly 0 Mb of data
29: <D> = 7.3593 Std. Dev. = 9.7910 Error = 5.6529
29: Fitting from 0.008 to 0.088 ps
29:
29: D[ mol] 7.8614 (+/- 1.5619) 1e-5 cm^2/s
29: [ OK ] MsdMolTest.diffMolSelected (4029 ms)
29: [----------] 3 tests from MsdMolTest (12139 ms total)
29:
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: trr version: GMX_trn_file (single precision)
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/0 (8 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/1 (9 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/2 (8 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from gro file '', 6 atoms.
29:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/3 (7 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000 't= 0.00000', 6 atoms
29:
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/4 (8 ms)
29: [ RUN ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5
29: Group 0 ( System) has 6 elements
29: Group 1 ( Water) has 6 elements
29: Group 2 ( SOL) has 6 elements
29: Select a group:
Reading frame 0 time 0.000
Reading frame 1 time 0.000
Last frame 1 time 0.000
29: Selected 0: 'System'
29: [ OK ] NoFatalErrorWhenWritingFrom/GmxTraj.WithDifferentInputFormats/5 (8 ms)
29: [----------] 6 tests from NoFatalErrorWhenWritingFrom/GmxTraj (48 ms total)
29:
29: [----------] Global test environment tear-down
29: [==========] 27 tests from 5 test cases ran. (12257 ms total)
29: [ PASSED ] 27 tests.
29/54 Test #29: GmxAnaTest .......................... Passed 12.34 sec
test 30
Start 30: GmxPreprocessTests
30: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxpreprocess-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxPreprocessTests.xml"
30: Test timeout computed to be: 30
30: [==========] Running 51 tests from 9 test cases.
30: [----------] Global test environment set-up.
30: [----------] 4 tests from GenconfTest
30: [ RUN ] GenconfTest.nbox_Works
30: [ OK ] GenconfTest.nbox_Works (43 ms)
30: [ RUN ] GenconfTest.nbox_norenumber_Works
30: [ OK ] GenconfTest.nbox_norenumber_Works (3 ms)
30: [ RUN ] GenconfTest.nbox_dist_Works
30: [ OK ] GenconfTest.nbox_dist_Works (4 ms)
30: [ RUN ] GenconfTest.nbox_rot_Works
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: center of geometry: 1.733667, 1.477000, 0.905167
30: [ OK ] GenconfTest.nbox_rot_Works (6 ms)
30: [----------] 4 tests from GenconfTest (56 ms total)
30:
30: [----------] 2 tests from GenionTest
30: [ RUN ] GenionTest.HighConcentrationIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to -1677738289
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_HighConcentrationIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
30: Group 0 ( System) has 653 elements
30: Group 1 ( Water) has 648 elements
30: Group 2 ( SOL) has 648 elements
30: Group 3 ( non-Water) has 5 elements
30: Group 4 ( Other) has 5 elements
30: Group 5 ( METH) has 5 elements
30: Select a group: Number of (3-atomic) solvent molecules: 216
30: Using random seed 1997.
30: Replacing solvent molecule 56 (atom 168) with NA
30: Replacing solvent molecule 120 (atom 360) with NA
30: Replacing solvent molecule 182 (atom 546) with NA
30: Replacing solvent molecule 71 (atom 213) with NA
30: Replacing solvent molecule 189 (atom 567) with CL
30: Replacing solvent molecule 54 (atom 162) with CL
30: Replacing solvent molecule 155 (atom 465) with CL
30: Replacing solvent molecule 99 (atom 297) with CL
30:
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: Will try to add 4 NA ions and 4 CL ions.
30: Select a continuous group of solvent molecules
30: Selected 1: 'Water'
30: [ OK ] GenionTest.HighConcentrationIonPlacement (4104 ms)
30: [ RUN ] GenionTest.NoIonPlacement
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet
30: buffer. The cluster pair list does have a buffering effect, but choosing
30: a larger rlist might be necessary for good energy conservation.
30:
30:
30: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: Setting the LD random seed to 1333458927
30: Generated 331705 of the 331705 non-bonded parameter combinations
30: Generating 1-4 interactions: fudge = 0.5
30: Generated 331705 of the 331705 1-4 parameter combinations
30: Excluding 2 bonded neighbours molecule type 'SOL'
30: Excluding 3 bonded neighbours molecule type 'methane'
30: Number of degrees of freedom in T-Coupling group rest is 1308.00
30:
30: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_input.mdp]:
30: You are using a plain Coulomb cut-off, which might produce artifacts.
30: You might want to consider using PME electrostatics.
30:
30:
30:
30: There were 3 notes
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
30: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GenionTest_NoIonPlacement_spc216_with_methane.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
30: No ions to add, will just copy input configuration.
30: Analysing residue names:
30: There are: 216 Water residues
30: There are: 1 Other residues
30: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
30: This run will generate roughly 0 Mb of data
30: [ OK ] GenionTest.NoIonPlacement (4293 ms)
30: [----------] 2 tests from GenionTest (8397 ms total)
30:
30: [----------] 1 test from GenRestrTest
30: [ RUN ] GenRestrTest.SimpleRestraintsGenerated
30:
30: Reading structure file
30: Group 0 ( System) has 156 elements
30: Group 1 ( Protein) has 156 elements
30: Group 2 ( Protein-H) has 75 elements
30: Group 3 ( C-alpha) has 10 elements
30: Group 4 ( Backbone) has 30 elements
30: Group 5 ( MainChain) has 40 elements
30: Group 6 ( MainChain+Cb) has 49 elements
30: Group 7 ( MainChain+H) has 52 elements
30: Group 8 ( SideChain) has 104 elements
30: Group 9 ( SideChain-H) has 35 elements
30: Select a group: Select group to position restrain
30: Selected 3: 'C-alpha'
30: [ OK ] GenRestrTest.SimpleRestraintsGenerated (12 ms)
30: [----------] 1 test from GenRestrTest (12 ms total)
30:
30: [----------] 9 tests from PreprocessingAtomTypesTest
30: [ RUN ] PreprocessingAtomTypesTest.EmptyOnCreate
30: [ OK ] PreprocessingAtomTypesTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingAtomTypesTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddTypeWorks
30: [ OK ] PreprocessingAtomTypesTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingAtomTypesTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingAtomTypesTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFound
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.WrongNameNotFound
30: [ OK ] PreprocessingAtomTypesTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingAtomTypesTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 9 tests from PreprocessingAtomTypesTest (1 ms total)
30:
30: [----------] 10 tests from PreprocessingBondAtomTypeTest
30: [ RUN ] PreprocessingBondAtomTypeTest.EmptyOnCreate
30: [ OK ] PreprocessingBondAtomTypeTest.EmptyOnCreate (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid
30: [ OK ] PreprocessingBondAtomTypeTest.IndexOutOfRangeInvalid (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddTypeWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddTypeWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks
30: [ OK ] PreprocessingBondAtomTypeTest.AddMultipleTypesWorks (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry
30: [ OK ] PreprocessingBondAtomTypeTest.CannotAddDuplicateEntry (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType
30: [ OK ] PreprocessingBondAtomTypeTest.ReturnsCorrectIndexOnDuplicateType (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFound
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.WrongNameNotFound
30: [ OK ] PreprocessingBondAtomTypeTest.WrongNameNotFound (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.CorrectNameFromTypeNumber (0 ms)
30: [ RUN ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber
30: [ OK ] PreprocessingBondAtomTypeTest.NoNameFromIncorrectTypeNumber (0 ms)
30: [----------] 10 tests from PreprocessingBondAtomTypeTest (0 ms total)
30:
30: [----------] 5 tests from InsertMoleculesTest
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
30: Added 1 molecules (out of 1 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro
30:
30: Output configuration contains 8 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (70 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3 success (now 6 atoms)!
30:
Try 4 success (now 8 atoms)!
30:
Try 5 success (now 10 atoms)!
30:
30: Added 5 molecules (out of 5 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro
30:
30: Output configuration contains 10 atoms in 10 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (8 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 8 atoms)!
30:
Try 2 success (now 10 atoms)!
30:
30: Added 2 molecules (out of 2 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro
30:
30: Output configuration contains 10 atoms in 4 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (8 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement
30: Reading solute configuration
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30:
Try 1 success (now 650 atoms)!
30:
Try 2 success (now 652 atoms)!
30:
Try 3 success (now 654 atoms)!
30:
Try 4 success (now 656 atoms)!
30:
30: Added 4 molecules (out of 4 requested)
30: Replaced 8 residues (24 atoms)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro
30:
30: Output configuration contains 632 atoms in 212 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (60 ms)
30: [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Using random seed 1997
30: Read 4 positions from file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat
30:
30:
Try 1 success (now 2 atoms)!
30:
Try 2 success (now 4 atoms)!
30:
Try 3
Try 4
Try 5
Try 6
Try 7
Try 8
Try 9
Try 10
Try 11
Try 12 skipped position (0.990, 2.010, 3.000)
30:
Try 13 success (now 6 atoms)!
30:
30: Added 3 molecules (out of 4 requested)
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro
30:
30: Output configuration contains 6 atoms in 3 residues
30: [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (9 ms)
30: [----------] 5 tests from InsertMoleculesTest (156 ms total)
30:
30: [----------] 14 tests from GetIrTest
30: [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines
30: Ignoring obsolete mdp entry 'title'
30: Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps'
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (32 ms)
30: [ RUN ] GetIrTest.RejectsNonCommentLineWithNoEquals
30: [ OK ] GetIrTest.RejectsNonCommentLineWithNoEquals (29 ms)
30: [ RUN ] GetIrTest.AcceptsKeyWithoutValue
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsKeyWithoutValue_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsKeyWithoutValue (23 ms)
30: [ RUN ] GetIrTest.RejectsValueWithoutKey
30: [ OK ] GetIrTest.RejectsValueWithoutKey (30 ms)
30: [ RUN ] GetIrTest.RejectsEmptyKeyAndEmptyValue
30: [ OK ] GetIrTest.RejectsEmptyKeyAndEmptyValue (54 ms)
30: [ RUN ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsDefineParametersWithValuesIncludingAssignment_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsDefineParametersWithValuesIncludingAssignment (18 ms)
30: [ RUN ] GetIrTest.AcceptsEmptyLines
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsEmptyLines_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsEmptyLines (30 ms)
30: [ RUN ] GetIrTest.AcceptsElectricField
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricField_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricField (19 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldPulsed
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldPulsed_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldPulsed (32 ms)
30: [ RUN ] GetIrTest.AcceptsElectricFieldOscillating
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsElectricFieldOscillating_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsElectricFieldOscillating (19 ms)
30: [ RUN ] GetIrTest.RejectsDuplicateOldAndNewKeys
30: [ OK ] GetIrTest.RejectsDuplicateOldAndNewKeys (13 ms)
30: [ RUN ] GetIrTest.AcceptsImplicitSolventNo
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsImplicitSolventNo_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsImplicitSolventNo (20 ms)
30: [ RUN ] GetIrTest.RejectsImplicitSolventYes
30: [ OK ] GetIrTest.RejectsImplicitSolventYes (32 ms)
30: [ RUN ] GetIrTest.AcceptsMimic
30:
30: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_AcceptsMimic_input.mdp]:
30: For a correct single-point energy evaluation with nsteps = 0, use
30: continuation = yes to avoid constraining the input coordinates.
30:
30: [ OK ] GetIrTest.AcceptsMimic (20 ms)
30: [----------] 14 tests from GetIrTest (371 ms total)
30:
30: [----------] 5 tests from SolvateTest
30: [ RUN ] SolvateTest.cs_box_Works
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 1x1x1 boxes
30: Solvent box contains 270 atoms in 90 residues
30: Removed 129 solvent atoms due to solvent-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 47 residues
30: Generated solvent containing 141 atoms in 47 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_box_Works_out.gro
30:
30: Output configuration contains 141 atoms in 47 residues
30: Volume : 1.331 (nm^3)
30: Density : 1056.36 (g/l)
30: Number of solvent molecules: 47
30:
30: [ OK ] SolvateTest.cs_box_Works (53 ms)
30: [ RUN ] SolvateTest.cs_cp_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: [ OK ] SolvateTest.cs_cp_Works (275 ms)
30: [ RUN ] SolvateTest.cs_cp_p_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 886 residues
30: Generated solvent containing 2658 atoms in 886 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_out.gro
30:
30: Output configuration contains 2664 atoms in 888 residues
30: Volume : 27.2709 (nm^3)
30: Density : 974.777 (g/l)
30: Number of solvent molecules: 886
30:
30: Processing topology
30: Adding line for 886 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_cs_cp_p_Works_spc-and-methanol.top)
30: [ OK ] SolvateTest.cs_cp_p_Works (277 ms)
30: [ RUN ] SolvateTest.shell_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 2x2x2 boxes
30: Solvent box contains 3660 atoms in 1220 residues
30: Removed 987 solvent atoms due to solvent-solvent overlap
30: Removed 1902 solvent atoms more than 1.000000 nm from solute.
30: Removed 15 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 1 molecule type:
30: SOL ( 3 atoms): 252 residues
30: Generated solvent containing 756 atoms in 252 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_shell_Works_out.gro
30:
30: Output configuration contains 762 atoms in 254 residues
30: Volume : 27.2709 (nm^3)
30: Density : 279.3 (g/l)
30: Number of solvent molecules: 252
30:
30: [ OK ] SolvateTest.shell_Works (135 ms)
30: [ RUN ] SolvateTest.update_Topology_Works
30: Reading solute configuration
30: Reading solvent configuration
30:
30: Initialising inter-atomic distances...
30:
30: WARNING: Masses and atomic (Van der Waals) radii will be guessed
30: based on residue and atom names, since they could not be
30: definitively assigned from the information in your input
30: files. These guessed numbers might deviate from the mass
30: and radius of the atom type. Please check the output
30: files if necessary.
30:
30: NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii
30: from the source below. This means the results may be different
30: compared to previous GROMACS versions.
30:
30: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
30: A. Bondi
30: van der Waals Volumes and Radii
30: J. Phys. Chem. 68 (1964) pp. 441-451
30: -------- -------- --- Thank You --- -------- --------
30:
30: Generating solvent configuration
30: Will generate new solvent configuration of 3x3x3 boxes
30: Solvent box contains 14952 atoms in 4984 residues
30: Removed 2787 solvent atoms due to solvent-solvent overlap
30: Removed 30 solvent atoms due to solute-solvent overlap
30: Sorting configuration
30: Found 2 different molecule types:
30: HOH ( 3 atoms): 1876 residues
30: SOL ( 3 atoms): 2169 residues
30: Generated solvent containing 0 atoms in 0 residues
30: Writing generated configuration to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_out.gro
30:
30: Output configuration contains 12141 atoms in 4047 residues
30: Volume : 125 (nm^3)
30: Density : 968.963 (g/l)
30: Number of solvent molecules: 4045
30:
30: Processing topology
30: Adding line for 1876 solvent molecules with resname (HOH) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: Adding line for 2169 solvent molecules with resname (SOL) to topology file (/<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/gmxpreprocess/tests/Testing/Temporary/SolvateTest_update_Topology_Works_simple.top)
30: [ OK ] SolvateTest.update_Topology_Works (1126 ms)
30: [----------] 5 tests from SolvateTest (1866 ms total)
30:
30: [----------] 1 test from TopDirTests
30: [ RUN ] TopDirTests.NamesArrayHasCorrectSize
30: [ OK ] TopDirTests.NamesArrayHasCorrectSize (0 ms)
30: [----------] 1 test from TopDirTests (0 ms total)
30:
30: [----------] Global test environment tear-down
30: [==========] 51 tests from 9 test cases ran. (10860 ms total)
30: [ PASSED ] 51 tests.
30/54 Test #30: GmxPreprocessTests .................. Passed 10.93 sec
test 31
Start 31: Pdb2gmx1Test
31: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx1-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx1Test.xml"
31: Test timeout computed to be: 30
31: [==========] Running 24 tests from 1 test case.
31: [----------] Global test environment set-up.
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/0 (580 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/1 (647 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/2 (523 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/3 (575 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/4 (549 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/5 (712 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/6 (568 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip3p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/7 (572 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/8 (565 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/9 (584 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/10 (639 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/11 (487 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/12 (552 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/13 (612 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/14 (574 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip4p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/15 (523 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 0 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/16 (518 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 0 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/17 (575 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 0 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/18 (529 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 0 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/19 (493 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 25 donors and 23 acceptors were found.
31: There are 41 hydrogen bonds
31: Will use HISE for residue 8
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS3 HIS8
31: SG9 NE251
31: HIS8 NE251 1.055
31: MET12 SD83 0.763 0.990
31: Making bonds...
31: Number of bonds was 254, now 254
31: Marked 124 virtual sites
31: Added 16 dummy masses
31: Added 26 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 653 pairs
31: Before cleaning: 663 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 663 dihedrals, 51 impropers, 457 angles
31: 650 pairs, 254 bonds and 130 virtual sites
31: Total mass 1846.112 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
31: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 128
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (128 atoms, 16 residues)
31: Identified residue ALA2 as a starting terminus.
31: Identified residue SER17 as a ending terminus.
31: Start terminus ALA-2: NH3+
31: End terminus SER-17: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 252 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/20 (557 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 30 donors and 22 acceptors were found.
31: There are 36 hydrogen bonds
31: Will use HISE for residue 29
31: Will use HISE for residue 32
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: CYS27 HIS29
31: SG90 NE2111
31: HIS29 NE2111 0.987
31: HIS32 NE2135 1.590 1.155
31: Making bonds...
31: Number of bonds was 290, now 290
31: Marked 132 virtual sites
31: Added 10 dummy masses
31: Added 19 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 748 pairs
31: Before cleaning: 778 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 778 dihedrals, 72 impropers, 516 angles
31: 736 pairs, 290 bonds and 133 virtual sites
31: Total mass 2088.357 a.m.u.
31: Total charge 1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
31: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 149
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (149 atoms, 16 residues)
31: Identified residue THR18 as a starting terminus.
31: Identified residue PHE33 as a ending terminus.
31: Start terminus THR-18: NH3+
31: End terminus PHE-33: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 281 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/21 (638 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 22 acceptors were found.
31: There are 26 hydrogen bonds
31: Will use HISE for residue 45
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS45
31: NE295
31: MET46 SD102 1.078
31: Making bonds...
31: Number of bonds was 261, now 261
31: Marked 123 virtual sites
31: Added 22 dummy masses
31: Added 35 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 676 pairs
31: Before cleaning: 696 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 696 dihedrals, 56 impropers, 472 angles
31: 667 pairs, 261 bonds and 132 virtual sites
31: Total mass 1861.128 a.m.u.
31: Total charge -1.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
31: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 132
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (132 atoms, 16 residues)
31: Identified residue ALA34 as a starting terminus.
31: Identified residue ALA49 as a ending terminus.
31: Start terminus ALA-34: NH3+
31: End terminus ALA-49: COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 255 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/22 (592 ms)
31: [ RUN ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.r2b
31: All occupancies are one
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/atomtypes.atp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.rtp
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.hdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.n.tdb
31: Opening force field file /<<PKGBUILDDIR>>/share/top/oplsaa.ff/aminoacids.c.tdb
31: Analysing hydrogen-bonding network for automated assignment of histidine
31: protonation. 22 donors and 21 acceptors were found.
31: There are 30 hydrogen bonds
31: Will use HISE for residue 60
31: 8 out of 8 lines of specbond.dat converted successfully
31: Special Atom Distance matrix:
31: HIS60
31: NE285
31: CYS62 SG98 0.803
31: Making bonds...
31: Number of bonds was 232, now 232
31: Marked 111 virtual sites
31: Added 18 dummy masses
31: Added 31 new constraints
31: Generating angles, dihedrals and pairs...
31: Before cleaning: 603 pairs
31: Before cleaning: 618 dihedrals
31: Keeping all generated dihedrals
31: Making cmap torsions...
31: There are 618 dihedrals, 48 impropers, 419 angles
31: 597 pairs, 232 bonds and 116 virtual sites
31: Total mass 1662.883 a.m.u.
31: Total charge 0.000 e
31: Writing topology
31:
31: Writing coordinate file...
31:
31: Using the Oplsaa force field in directory oplsaa.ff
31:
31: going to rename oplsaa.ff/aminoacids.r2b
31: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
31: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
31: Analyzing pdb file
31: Splitting chemical chains based on TER records or chain id changing.
31: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
31:
31: chain #res #atoms
31: 1 ' ' 16 117
31:
31: Reading residue database... (Oplsaa)
31: Processing chain 1 (117 atoms, 16 residues)
31: Identified residue LYS50 as a starting terminus.
31: Identified residue PRO65 as a ending terminus.
31: Start terminus LYS-50: NH3+
31: End terminus PRO-65: PRO-COO-
31: Checking for duplicate atoms....
31: Generating any missing hydrogen atoms and/or adding termini.
31: Now there are 16 residues with 228 atoms
31: --------- PLEASE NOTE ------------
31: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
31: The Oplsaa force field and the tip5p water model are used.
31: --------- ETON ESAELP ------------
31: [ OK ] ForOplsaa/Pdb2gmxTest.ProducesMatchingTopology/23 (580 ms)
31: [----------] 24 tests from ForOplsaa/Pdb2gmxTest (13749 ms total)
31:
31: [----------] Global test environment tear-down
31: [==========] 24 tests from 1 test case ran. (13750 ms total)
31: [ PASSED ] 24 tests.
31/54 Test #31: Pdb2gmx1Test ........................ Passed 13.82 sec
test 32
Start 32: Pdb2gmx2Test
32: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx2-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx2Test.xml"
32: Test timeout computed to be: 30
32: [==========] Running 32 tests from 2 test cases.
32: [----------] Global test environment set-up.
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/0 (344 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/1 (435 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/2 (323 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/3 (290 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/4 (345 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/5 (442 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/6 (324 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/7 (305 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/8 (356 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/9 (430 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/10 (326 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/11 (289 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 172, now 167
32: Marked 37 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 305 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 77 impropers, 241 angles
32: 267 pairs, 167 bonds and 37 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 165 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/12 (367 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 216, now 211
32: Marked 53 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 429 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 134 impropers, 316 angles
32: 273 pairs, 211 bonds and 51 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 202 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/13 (422 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 179, now 174
32: Marked 36 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 349 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 102 impropers, 260 angles
32: 242 pairs, 174 bonds and 36 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 168 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/14 (326 ms)
32: [ RUN ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.rtp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos43a1.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 159, now 154
32: Marked 33 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 299 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 80 impropers, 227 angles
32: 232 pairs, 154 bonds and 31 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos43a1 force field in directory gromos43a1.ff
32:
32: going to rename gromos43a1.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos43a1)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 150 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos43a1 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos43a1/Pdb2gmxTest.ProducesMatchingTopology/15 (313 ms)
32: [----------] 16 tests from ForGromos43a1/Pdb2gmxTest (5640 ms total)
32:
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/0 (416 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/1 (408 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/2 (347 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/3 (394 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/4 (428 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/5 (404 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/6 (366 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spc water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/7 (331 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 0 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/8 (349 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 0 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/9 (431 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 0 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/10 (341 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 0 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/11 (321 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 25 donors and 23 acceptors were found.
32: There are 41 hydrogen bonds
32: Will use HISE for residue 8
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS3 HIS8
32: SG9 NE251
32: HIS8 NE251 1.055
32: MET12 SD83 0.763 0.990
32: Making bonds...
32: Number of bonds was 174, now 169
32: Marked 39 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named SER of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 267 pairs
32: Before cleaning: 312 dihedrals
32: Making cmap torsions...
32: There are 90 dihedrals, 79 impropers, 245 angles
32: 267 pairs, 169 bonds and 39 virtual sites
32: Total mass 1846.116 a.m.u.
32: Total charge 0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
32: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 128
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (128 atoms, 16 residues)
32: Identified residue ALA2 as a starting terminus.
32: Identified residue SER17 as a ending terminus.
32: Start terminus ALA-2: NH3+
32: End terminus SER-17: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 167 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/12 (357 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 30 donors and 22 acceptors were found.
32: There are 36 hydrogen bonds
32: Will use HISE for residue 29
32: Will use HISE for residue 32
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: CYS27 HIS29
32: SG90 NE2111
32: HIS29 NE2111 0.987
32: HIS32 NE2135 1.590 1.155
32: Making bonds...
32: Number of bonds was 220, now 215
32: Marked 57 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named THR of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PHE of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 273 pairs
32: Before cleaning: 443 dihedrals
32: Making cmap torsions...
32: There are 93 dihedrals, 138 impropers, 324 angles
32: 273 pairs, 215 bonds and 55 virtual sites
32: Total mass 2088.361 a.m.u.
32: Total charge 1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
32: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 149
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (149 atoms, 16 residues)
32: Identified residue THR18 as a starting terminus.
32: Identified residue PHE33 as a ending terminus.
32: Start terminus THR-18: NH3+
32: End terminus PHE-33: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 206 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/13 (409 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 22 acceptors were found.
32: There are 26 hydrogen bonds
32: Will use HISE for residue 45
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS45
32: NE295
32: MET46 SD102 1.078
32: Making bonds...
32: Number of bonds was 181, now 176
32: Marked 38 virtual sites
32: Added 4 dummy masses
32: Added 8 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named ALA of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 242 pairs
32: Before cleaning: 356 dihedrals
32: Making cmap torsions...
32: There are 81 dihedrals, 104 impropers, 264 angles
32: 242 pairs, 176 bonds and 38 virtual sites
32: Total mass 1861.132 a.m.u.
32: Total charge -1.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
32: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 132
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (132 atoms, 16 residues)
32: Identified residue ALA34 as a starting terminus.
32: Identified residue ALA49 as a ending terminus.
32: Start terminus ALA-34: NH3+
32: End terminus ALA-49: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 170 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/14 (354 ms)
32: [ RUN ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.r2b
32: All occupancies are one
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/atomtypes.atp
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.rtp
32: Using default: not generating all possible dihedrals
32: Using default: excluding 3 bonded neighbors
32: Using default: generating 1,4 H--H interactions
32: Using default: removing proper dihedrals found on the same bond as a proper dihedral
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.hdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.n.tdb
32: Opening force field file /<<PKGBUILDDIR>>/share/top/gromos53a6.ff/aminoacids.c.tdb
32: Analysing hydrogen-bonding network for automated assignment of histidine
32: protonation. 22 donors and 21 acceptors were found.
32: There are 30 hydrogen bonds
32: Will use HISE for residue 60
32: 8 out of 8 lines of specbond.dat converted successfully
32: Special Atom Distance matrix:
32: HIS60
32: NE285
32: CYS62 SG98 0.803
32: Making bonds...
32: Number of bonds was 161, now 156
32: Marked 35 virtual sites
32: Added 4 dummy masses
32: Added 10 new constraints
32: Generating angles, dihedrals and pairs...
32:
32: WARNING: WARNING: Residue 1 named LYS of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom H used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32:
32: WARNING: WARNING: Residue 16 named PRO of a molecule in the input file was mapped
32: to an entry in the topology database, but the atom O used in
32: an interaction of type angle in that entry is not found in the
32: input file. Perhaps your atom and/or residue naming needs to be
32: fixed.
32:
32:
32: Before cleaning: 232 pairs
32: Before cleaning: 306 dihedrals
32: Making cmap torsions...
32: There are 78 dihedrals, 82 impropers, 231 angles
32: 232 pairs, 156 bonds and 33 virtual sites
32: Total mass 1662.887 a.m.u.
32: Total charge -0.000 e
32: Writing topology
32:
32: Writing coordinate file...
32:
32: Using the Gromos53a6 force field in directory gromos53a6.ff
32:
32: going to rename gromos53a6.ff/aminoacids.r2b
32: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
32: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
32: Analyzing pdb file
32: Splitting chemical chains based on TER records or chain id changing.
32: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
32:
32: chain #res #atoms
32: 1 ' ' 16 117
32:
32: Reading residue database... (Gromos53a6)
32: Processing chain 1 (117 atoms, 16 residues)
32: Identified residue LYS50 as a starting terminus.
32: Identified residue PRO65 as a ending terminus.
32: Start terminus LYS-50: NH3+
32: End terminus PRO-65: COO-
32: Checking for duplicate atoms....
32: Generating any missing hydrogen atoms and/or adding termini.
32: Now there are 16 residues with 152 atoms
32: --------- PLEASE NOTE ------------
32: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
32: The Gromos53a6 force field and the spce water model are used.
32: --------- ETON ESAELP ------------
32: [ OK ] ForGromos53a6/Pdb2gmxTest.ProducesMatchingTopology/15 (330 ms)
32: [----------] 16 tests from ForGromos53a6/Pdb2gmxTest (5989 ms total)
32:
32: [----------] Global test environment tear-down
32: [==========] 32 tests from 2 test cases ran. (11629 ms total)
32: [ PASSED ] 32 tests.
32/54 Test #32: Pdb2gmx2Test ........................ Passed 11.70 sec
test 33
Start 33: Pdb2gmx3Test
33: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/pdb2gmx3-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/Pdb2gmx3Test.xml"
33: Test timeout computed to be: 30
33: [==========] Running 28 tests from 4 test cases.
33: [----------] Global test environment set-up.
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/0 (441 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/1 (490 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/2 (545 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/3 (397 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 255, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 691 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 691 dihedrals, 51 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.132 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/4 (496 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 291, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 788 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 788 dihedrals, 72 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.366 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/5 (552 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 262, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 727 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 727 dihedrals, 56 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.124 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/6 (489 ms)
33: [ RUN ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/amber99sb-ildn.ff/rna.arn
33: Making bonds...
33: Number of bonds was 233, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 634 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 634 dihedrals, 48 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.888 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Amber99sb-ildn force field in directory amber99sb-ildn.ff
33:
33: going to rename amber99sb-ildn.ff/aminoacids.r2b
33: going to rename amber99sb-ildn.ff/dna.r2b
33: going to rename amber99sb-ildn.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Amber99sb-ildn)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Amber99sb-ildn force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForAmber99sb_ildn/Pdb2gmxTest.ProducesMatchingTopology/7 (433 ms)
33: [----------] 8 tests from ForAmber99sb_ildn/Pdb2gmxTest (3843 ms total)
33:
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 0 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/0 (427 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 0 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/1 (489 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 0 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/2 (435 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 0 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/3 (395 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 254, now 254
33: Marked 124 virtual sites
33: Added 16 dummy masses
33: Added 26 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 653 pairs
33: Before cleaning: 663 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 663 dihedrals, 48 impropers, 457 angles
33: 650 pairs, 254 bonds and 130 virtual sites
33: Total mass 1846.115 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 128 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 128 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 128
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (128 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 252 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment1.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/4 (464 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 30 donors and 22 acceptors were found.
33: There are 36 hydrogen bonds
33: Will use HISE for residue 29
33: Will use HISE for residue 32
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS27 HIS29
33: SG90 NE2111
33: HIS29 NE2111 0.987
33: HIS32 NE2135 1.590 1.155
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 290, now 290
33: Marked 132 virtual sites
33: Added 10 dummy masses
33: Added 19 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 748 pairs
33: Before cleaning: 778 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 778 dihedrals, 49 impropers, 516 angles
33: 736 pairs, 290 bonds and 133 virtual sites
33: Total mass 2088.361 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb...
33: Read 'Protein (second fragment of regressiontests/complex/aminoacids.gro)', 149 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 149 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 149
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (149 atoms, 16 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue PHE33 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus PHE-33: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 281 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment2.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/5 (517 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 22 acceptors were found.
33: There are 26 hydrogen bonds
33: Will use HISE for residue 45
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS45
33: NE295
33: MET46 SD102 1.078
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 261, now 261
33: Marked 123 virtual sites
33: Added 22 dummy masses
33: Added 35 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 676 pairs
33: Before cleaning: 696 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 696 dihedrals, 39 impropers, 472 angles
33: 667 pairs, 261 bonds and 132 virtual sites
33: Total mass 1861.130 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb...
33: Read 'Protein (third fragment of regressiontests/complex/aminoacids.gro)', 132 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 132 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 132
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (132 atoms, 16 residues)
33: Identified residue ALA34 as a starting terminus.
33: Identified residue ALA49 as a ending terminus.
33: Start terminus ALA-34: NH3+
33: End terminus ALA-49: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment3.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/6 (481 ms)
33: [ RUN ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 22 donors and 21 acceptors were found.
33: There are 30 hydrogen bonds
33: Will use HISE for residue 60
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS60
33: NE285
33: CYS62 SG98 0.803
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 232, now 232
33: Marked 111 virtual sites
33: Added 18 dummy masses
33: Added 31 new constraints
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 603 pairs
33: Before cleaning: 618 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 14 cmap torsion pairs
33: There are 618 dihedrals, 38 impropers, 419 angles
33: 597 pairs, 232 bonds and 116 virtual sites
33: Total mass 1662.885 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb...
33: Read 'Protein (fourth fragment of regressiontests/complex/aminoacids.gro)', 117 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 1 chains and 0 blocks of water and 16 residues with 117 atoms
33:
33: chain #res #atoms
33: 1 ' ' 16 117
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 (117 atoms, 16 residues)
33: Identified residue LYS50 as a starting terminus.
33: Identified residue PRO65 as a ending terminus.
33: Start terminus LYS-50: NH3+
33: End terminus PRO-65: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 228 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/fragment4.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ForCharmm27/Pdb2gmxTest.ProducesMatchingTopology/7 (438 ms)
33: [----------] 8 tests from ForCharmm27/Pdb2gmxTest (3647 ms total)
33:
33: [----------] 8 tests from ChainSep/Pdb2gmxTest
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/0 (438 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 7 acceptors were found.
33: There are 7 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: HIS8
33: NE223
33: MET12 SD55 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 125, now 125
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 317 pairs
33: Before cleaning: 322 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 5 cmap torsion pairs
33: There are 322 dihedrals, 19 impropers, 227 angles
33: 314 pairs, 125 bonds and 0 virtual sites
33: Total mass 846.083 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 7 58
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (58 atoms, 7 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 7 residues with 124 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 124 atoms 7 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/1 (302 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 258, now 258
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 651 pairs
33: Before cleaning: 661 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 10 cmap torsion pairs
33: There are 661 dihedrals, 46 impropers, 463 angles
33: 648 pairs, 258 bonds and 0 virtual sites
33: Total mass 1882.146 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33:
33: Merged chains into joint molecule definitions at 2 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 258 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/2 (440 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 10 donors and 12 acceptors were found.
33: There are 13 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3
33: SG9
33: HIS8 NE251 1.055
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 115, now 115
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 288 pairs
33: Before cleaning: 293 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 6 cmap torsion pairs
33: There are 293 dihedrals, 23 impropers, 203 angles
33: 285 pairs, 115 bonds and 0 virtual sites
33: Total mass 888.952 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 258 atoms and 16 residues
33: Total mass in system 1882.146 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 3 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 8 61
33: 2 'B' 3 25
33: 3 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (61 atoms, 8 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 8 residues with 114 atoms
33: Chain time...
33: Processing chain 2 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 3 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 114 atoms 8 residues
33: Including chain 2 in system: 61 atoms 3 residues
33: Including chain 3 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/3 (298 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 260, now 260
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 650 pairs
33: Before cleaning: 660 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 8 cmap torsion pairs
33: There are 660 dihedrals, 45 impropers, 466 angles
33: 647 pairs, 260 bonds and 0 virtual sites
33: Total mass 1900.162 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33:
33: Merged chains into joint molecule definitions at 3 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 261 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/4 (443 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 50, now 50
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 123 pairs
33: Before cleaning: 123 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 123 dihedrals, 9 impropers, 88 angles
33: 123 pairs, 50 bonds and 0 virtual sites
33: Total mass 434.421 a.m.u.
33: Total charge -2.000 e
33: Writing topology
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 6 donors and 4 acceptors were found.
33: There are 3 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 67, now 67
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 164 pairs
33: Before cleaning: 169 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 2 cmap torsion pairs
33: There are 169 dihedrals, 13 impropers, 118 angles
33: 161 pairs, 67 bonds and 0 virtual sites
33: Total mass 472.547 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 60, now 60
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 152 pairs
33: Before cleaning: 152 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 152 dihedrals, 5 impropers, 112 angles
33: 152 pairs, 60 bonds and 0 virtual sites
33: Total mass 391.552 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 261 atoms and 16 residues
33: Total mass in system 1900.162 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: WARNING: Chain identifier 'B' is used in two non-sequential blocks.
33: They will be treated as separate chains unless you reorder your file.
33: There are 4 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 4 28
33: 2 'B' 4 33
33: 3 'B' 3 25
33: 4 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (28 atoms, 4 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue GLU5 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus GLU-5: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 51 atoms
33: Chain time...
33: Processing chain 2 'B' (33 atoms, 4 residues)
33: Identified residue PHE6 as a starting terminus.
33: Identified residue ILE9 as a ending terminus.
33: Start terminus PHE-6: NH3+
33: End terminus ILE-9: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 4 residues with 66 atoms
33: Chain time...
33: Processing chain 3 'B' (25 atoms, 3 residues)
33: Identified residue LYS10 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus LYS-10: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 61 atoms
33: Chain time...
33: Processing chain 4 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 51 atoms 4 residues
33: Including chain 2 in system: 66 atoms 4 residues
33: Including chain 3 in system: 61 atoms 3 residues
33: Including chain 4 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/5 (297 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 25 donors and 23 acceptors were found.
33: There are 41 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 256, now 256
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 652 pairs
33: Before cleaning: 662 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 12 cmap torsion pairs
33: There are 662 dihedrals, 47 impropers, 460 angles
33: 649 pairs, 256 bonds and 0 virtual sites
33: Total mass 1864.131 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33:
33: Merged chains into joint molecule definitions at 1 places.
33:
33: There are 1 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 16 127
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (127 atoms, 16 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 16 residues with 255 atoms
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/6 (437 ms)
33: [ RUN ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: Analysing hydrogen-bonding network for automated assignment of histidine
33: protonation. 14 donors and 15 acceptors were found.
33: There are 20 hydrogen bonds
33: Will use HISE for residue 8
33: 8 out of 8 lines of specbond.dat converted successfully
33: Special Atom Distance matrix:
33: CYS3 HIS8
33: SG9 NE251
33: HIS8 NE251 1.055
33: MET12 SD83 0.763 0.990
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 173, now 173
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 441 pairs
33: Before cleaning: 446 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 9 cmap torsion pairs
33: There are 446 dihedrals, 29 impropers, 312 angles
33: 438 pairs, 173 bonds and 0 virtual sites
33: Total mass 1262.488 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 83, now 83
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 211 pairs
33: Before cleaning: 216 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 3 cmap torsion pairs
33: There are 216 dihedrals, 18 impropers, 148 angles
33: 211 pairs, 83 bonds and 0 virtual sites
33: Total mass 601.643 a.m.u.
33: Total charge 1.000 e
33: Writing topology
33: Now there are 255 atoms and 16 residues
33: Total mass in system 1864.131 a.m.u.
33: Total charge in system 0.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb...
33: Read 'Protein (first fragment of regressiontests/complex/aminoacids.gro)', 127 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 16 residues with 127 atoms
33:
33: chain #res #atoms
33: 1 'A' 11 86
33: 2 'C' 5 41
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (86 atoms, 11 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue MET12 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus MET-12: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 11 residues with 172 atoms
33: Chain time...
33: Processing chain 2 'C' (41 atoms, 5 residues)
33: Identified residue ASN13 as a starting terminus.
33: Identified residue SER17 as a ending terminus.
33: Start terminus ASN-13: NH3+
33: End terminus SER-17: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 5 residues with 83 atoms
33: Chain time...
33: Including chain 1 in system: 172 atoms 11 residues
33: Including chain 2 in system: 83 atoms 5 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/chainTer.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainSep/Pdb2gmxTest.ProducesMatchingTopology/7 (317 ms)
33: [----------] 8 tests from ChainSep/Pdb2gmxTest (2973 ms total)
33:
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on changing chain id only (ignoring TER records).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/0 (204 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records only (ignoring chain id).
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/1 (209 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records or chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/2 (205 ms)
33: [ RUN ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.r2b
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.r2b
33: All occupancies are one
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/atomtypes.atp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.rtp
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/lipids.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.hdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.n.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.c.tdb
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.c.tdb
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 35, now 35
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 83 pairs
33: Before cleaning: 83 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 83 dihedrals, 6 impropers, 61 angles
33: 83 pairs, 35 bonds and 0 virtual sites
33: Total mass 306.314 a.m.u.
33: Total charge -1.000 e
33: Writing topology
33: 8 out of 8 lines of specbond.dat converted successfully
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/aminoacids.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/dna.arn
33: Opening force field file /<<PKGBUILDDIR>>/share/top/charmm27.ff/rna.arn
33: Making bonds...
33: Number of bonds was 58, now 58
33: Generating angles, dihedrals and pairs...
33: Before cleaning: 145 pairs
33: Before cleaning: 150 dihedrals
33: Keeping all generated dihedrals
33: Making cmap torsions...
33: There are 1 cmap torsion pairs
33: There are 150 dihedrals, 5 impropers, 103 angles
33: 142 pairs, 58 bonds and 0 virtual sites
33: Total mass 404.468 a.m.u.
33: Total charge 0.000 e
33: Writing topology
33: Now there are 93 atoms and 6 residues
33: Total mass in system 710.782 a.m.u.
33: Total charge in system -1.000 e
33:
33: Writing coordinate file...
33:
33: Using the Charmm27 force field in directory charmm27.ff
33:
33: going to rename charmm27.ff/aminoacids.r2b
33: going to rename charmm27.ff/rna.r2b
33: Reading /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb...
33: Read 'Fragments of peptides and ions', 47 atoms
33: Analyzing pdb file
33: Splitting chemical chains based on TER records and chain id changing.
33: There are 2 chains and 0 blocks of water and 6 residues with 47 atoms
33:
33: chain #res #atoms
33: 1 'A' 3 19
33: 2 'B' 3 28
33:
33: Reading residue database... (Charmm27)
33: Processing chain 1 'A' (19 atoms, 3 residues)
33: Identified residue ALA2 as a starting terminus.
33: Identified residue ASP4 as a ending terminus.
33: Start terminus ALA-2: NH3+
33: End terminus ASP-4: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 36 atoms
33: Chain time...
33: Processing chain 2 'B' (28 atoms, 3 residues)
33: Identified residue THR18 as a starting terminus.
33: Identified residue TRP20 as a ending terminus.
33: Start terminus THR-18: NH3+
33: End terminus TRP-20: COO-
33: Checking for duplicate atoms....
33: Generating any missing hydrogen atoms and/or adding termini.
33: Now there are 3 residues with 57 atoms
33: Chain time...
33: Including chain 1 in system: 36 atoms 3 residues
33: Including chain 2 in system: 57 atoms 3 residues
33: --------- PLEASE NOTE ------------
33: You have successfully generated a topology from: /<<PKGBUILDDIR>>/src/gromacs/gmxpreprocess/tests/two-fragments.pdb.
33: The Charmm27 force field and the tip3p water model are used.
33: --------- ETON ESAELP ------------
33: [ OK ] ChainChanges/Pdb2gmxTest.ProducesMatchingTopology/3 (206 ms)
33: [----------] 4 tests from ChainChanges/Pdb2gmxTest (824 ms total)
33:
33: [----------] Global test environment tear-down
33: [==========] 28 tests from 4 test cases ran. (11288 ms total)
33: [ PASSED ] 28 tests.
33/54 Test #33: Pdb2gmx3Test ........................ Passed 11.36 sec
test 34
Start 34: CorrelationsTest
34: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/correlations-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CorrelationsTest.xml"
34: Test timeout computed to be: 30
34: [==========] Running 21 tests from 3 test cases.
34: [----------] Global test environment set-up.
34: [----------] 10 tests from AutocorrTest
34: [ RUN ] AutocorrTest.EacNormal
34: [ OK ] AutocorrTest.EacNormal (19 ms)
34: [ RUN ] AutocorrTest.EacNoNormalize
34: [ OK ] AutocorrTest.EacNoNormalize (10 ms)
34: [ RUN ] AutocorrTest.EacCos
34: [ OK ] AutocorrTest.EacCos (17 ms)
34: [ RUN ] AutocorrTest.EacVector
34: [ OK ] AutocorrTest.EacVector (24 ms)
34: [ RUN ] AutocorrTest.EacRcross
34: [ OK ] AutocorrTest.EacRcross (8 ms)
34: [ RUN ] AutocorrTest.EacP0
34: [ OK ] AutocorrTest.EacP0 (24 ms)
34: [ RUN ] AutocorrTest.EacP1
34: [ OK ] AutocorrTest.EacP1 (24 ms)
34: [ RUN ] AutocorrTest.EacP2
34: [ OK ] AutocorrTest.EacP2 (44 ms)
34: [ RUN ] AutocorrTest.EacP3
34: [ OK ] AutocorrTest.EacP3 (21 ms)
34: [ RUN ] AutocorrTest.EacP4
34: [ OK ] AutocorrTest.EacP4 (24 ms)
34: [----------] 10 tests from AutocorrTest (226 ms total)
34:
34: [----------] 1 test from ManyAutocorrelationTest
34: [ RUN ] ManyAutocorrelationTest.Empty
34: [ OK ] ManyAutocorrelationTest.Empty (0 ms)
34: [----------] 1 test from ManyAutocorrelationTest (0 ms total)
34:
34: [----------] 10 tests from ExpfitTest
34: [ RUN ] ExpfitTest.EffnEXP1
34: [ OK ] ExpfitTest.EffnEXP1 (4 ms)
34: [ RUN ] ExpfitTest.EffnEXP2
34: [ OK ] ExpfitTest.EffnEXP2 (6 ms)
34: [ RUN ] ExpfitTest.EffnEXPEXP
34: [ OK ] ExpfitTest.EffnEXPEXP (12 ms)
34: [ RUN ] ExpfitTest.EffnEXP5
34: [ OK ] ExpfitTest.EffnEXP5 (34 ms)
34: [ RUN ] ExpfitTest.EffnEXP7
34: [ OK ] ExpfitTest.EffnEXP7 (34 ms)
34: [ RUN ] ExpfitTest.EffnEXP9
34: [ OK ] ExpfitTest.EffnEXP9 (153 ms)
34: [ RUN ] ExpfitTest.EffnERF
34: [ OK ] ExpfitTest.EffnERF (18 ms)
34: [ RUN ] ExpfitTest.EffnERREST
34: [ OK ] ExpfitTest.EffnERREST (6 ms)
34: [ RUN ] ExpfitTest.EffnVAC
34: [ OK ] ExpfitTest.EffnVAC (68 ms)
34: [ RUN ] ExpfitTest.EffnPRES
34: [ OK ] ExpfitTest.EffnPRES (136 ms)
34: [----------] 10 tests from ExpfitTest (475 ms total)
34:
34: [----------] Global test environment tear-down
34: [==========] 21 tests from 3 test cases ran. (753 ms total)
34: [ PASSED ] 21 tests.
34/54 Test #34: CorrelationsTest .................... Passed 0.82 sec
test 35
Start 35: AnalysisDataUnitTests
35: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/analysisdata-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/AnalysisDataUnitTests.xml"
35: Test timeout computed to be: 30
35: [==========] Running 69 tests from 14 test cases.
35: [----------] Global test environment set-up.
35: [----------] 3 tests from AnalysisDataInitializationTest
35: [ RUN ] AnalysisDataInitializationTest.BasicInitialization
35: [ OK ] AnalysisDataInitializationTest.BasicInitialization (0 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultiColumnModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultiColumnModules (2 ms)
35: [ RUN ] AnalysisDataInitializationTest.ChecksMultipointModules
35: [ OK ] AnalysisDataInitializationTest.ChecksMultipointModules (0 ms)
35: [----------] 3 tests from AnalysisDataInitializationTest (2 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/0, where TypeParam = (anonymous namespace)::SimpleInputData
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsParallelModuleCorrectly (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsMixedModulesCorrectly (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/0.CallsColumnModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/0.CallsModuleCorrectlyWithOutOfOrderFrames (4 ms)
35: [ RUN ] AnalysisDataCommonTest/0.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.FullStorageWorks (1 ms)
35: [ RUN ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/0.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/0.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/0.LimitedStorageWorks (1 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/0 (21 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/1, where TypeParam = (anonymous namespace)::DataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsParallelModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/1.CallsColumnModuleCorrectly (3 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/1.CallsModuleCorrectlyWithOutOfOrderFrames (5 ms)
35: [ RUN ] AnalysisDataCommonTest/1.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/1.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/1.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/1.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/1 (25 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/2, where TypeParam = (anonymous namespace)::MultipointInputData
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsParallelModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/2.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/2.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/2.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.FullStorageWorks (3 ms)
35: [ RUN ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/2.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/2.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/2.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/2 (29 ms total)
35:
35: [----------] 8 tests from AnalysisDataCommonTest/3, where TypeParam = (anonymous namespace)::MultipointDataSetsInputData
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsParallelModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsMixedModulesCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly
35: [ OK ] AnalysisDataCommonTest/3.CallsColumnModuleCorrectly (4 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames
35: [ OK ] AnalysisDataCommonTest/3.CallsModuleCorrectlyWithOutOfOrderFrames (6 ms)
35: [ RUN ] AnalysisDataCommonTest/3.FullStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.FullStorageWorks (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData
35: [ OK ] AnalysisDataCommonTest/3.CanAddModuleAfterStoredData (2 ms)
35: [ RUN ] AnalysisDataCommonTest/3.LimitedStorageWorks
35: [ OK ] AnalysisDataCommonTest/3.LimitedStorageWorks (2 ms)
35: [----------] 8 tests from AnalysisDataCommonTest/3 (28 ms total)
35:
35: [----------] 4 tests from AnalysisArrayDataTest
35: [ RUN ] AnalysisArrayDataTest.CallsModuleCorrectly
35: [ OK ] AnalysisArrayDataTest.CallsModuleCorrectly (4 ms)
35: [ RUN ] AnalysisArrayDataTest.StorageWorks
35: [ OK ] AnalysisArrayDataTest.StorageWorks (2 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxis
35: [ OK ] AnalysisArrayDataTest.CanSetXAxis (0 ms)
35: [ RUN ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount
35: [ OK ] AnalysisArrayDataTest.CanSetXAxisBeforeRowCount (0 ms)
35: [----------] 4 tests from AnalysisArrayDataTest (6 ms total)
35:
35: [----------] 6 tests from AverageModuleTest
35: [ RUN ] AverageModuleTest.BasicTest
35: [ OK ] AverageModuleTest.BasicTest (5 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipointData
35: [ OK ] AverageModuleTest.HandlesMultipointData (5 ms)
35: [ RUN ] AverageModuleTest.HandlesMultipleDataSets
35: [ OK ] AverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [ RUN ] AverageModuleTest.HandlesDataSetAveraging
35: [ OK ] AverageModuleTest.HandlesDataSetAveraging (5 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeXAxis
35: [ OK ] AverageModuleTest.CanCustomizeXAxis (4 ms)
35: [ RUN ] AverageModuleTest.CanCustomizeNonUniformXAxis
35: [ OK ] AverageModuleTest.CanCustomizeNonUniformXAxis (4 ms)
35: [----------] 6 tests from AverageModuleTest (30 ms total)
35:
35: [----------] 2 tests from FrameAverageModuleTest
35: [ RUN ] FrameAverageModuleTest.BasicTest
35: [ OK ] FrameAverageModuleTest.BasicTest (4 ms)
35: [ RUN ] FrameAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] FrameAverageModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 2 tests from FrameAverageModuleTest (10 ms total)
35:
35: [----------] 7 tests from AnalysisHistogramSettingsTest
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromBinsWithIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCount (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidth (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinCountAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithBinWidthAndIntegerBins (0 ms)
35: [ RUN ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange
35: [ OK ] AnalysisHistogramSettingsTest.InitializesFromRangeWithRoundedRange (0 ms)
35: [----------] 7 tests from AnalysisHistogramSettingsTest (0 ms total)
35:
35: [----------] 2 tests from SimpleHistogramModuleTest
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectly
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectly (7 ms)
35: [ RUN ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] SimpleHistogramModuleTest.ComputesCorrectlyWithAll (7 ms)
35: [----------] 2 tests from SimpleHistogramModuleTest (14 ms total)
35:
35: [----------] 3 tests from WeightedHistogramModuleTest
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectly
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectly (7 ms)
35: [ RUN ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll
35: [ OK ] WeightedHistogramModuleTest.ComputesCorrectlyWithAll (6 ms)
35: [ RUN ] WeightedHistogramModuleTest.HandlesMultipleDataSets
35: [ OK ] WeightedHistogramModuleTest.HandlesMultipleDataSets (7 ms)
35: [----------] 3 tests from WeightedHistogramModuleTest (23 ms total)
35:
35: [----------] 3 tests from BinAverageModuleTest
35: [ RUN ] BinAverageModuleTest.ComputesCorrectly
35: [ OK ] BinAverageModuleTest.ComputesCorrectly (5 ms)
35: [ RUN ] BinAverageModuleTest.ComputesCorrectlyWithAll
35: [ OK ] BinAverageModuleTest.ComputesCorrectlyWithAll (5 ms)
35: [ RUN ] BinAverageModuleTest.HandlesMultipleDataSets
35: [ OK ] BinAverageModuleTest.HandlesMultipleDataSets (6 ms)
35: [----------] 3 tests from BinAverageModuleTest (17 ms total)
35:
35: [----------] 4 tests from AbstractAverageHistogramTest
35: [ RUN ] AbstractAverageHistogramTest.ClonesCorrectly
35: [ OK ] AbstractAverageHistogramTest.ClonesCorrectly (8 ms)
35: [ RUN ] AbstractAverageHistogramTest.ComputesCumulativeHistogram
35: [ OK ] AbstractAverageHistogramTest.ComputesCumulativeHistogram (7 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidth (6 ms)
35: [ RUN ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins
35: [ OK ] AbstractAverageHistogramTest.ResamplesAtDoubleBinWidthWithIntegerBins (6 ms)
35: [----------] 4 tests from AbstractAverageHistogramTest (28 ms total)
35:
35: [----------] 3 tests from LifetimeModuleTest
35: [ RUN ] LifetimeModuleTest.BasicTest
35: [ OK ] LifetimeModuleTest.BasicTest (4 ms)
35: [ RUN ] LifetimeModuleTest.CumulativeTest
35: [ OK ] LifetimeModuleTest.CumulativeTest (4 ms)
35: [ RUN ] LifetimeModuleTest.HandlesMultipleDataSets
35: [ OK ] LifetimeModuleTest.HandlesMultipleDataSets (5 ms)
35: [----------] 3 tests from LifetimeModuleTest (13 ms total)
35:
35: [----------] Global test environment tear-down
35: [==========] 69 tests from 14 test cases ran. (248 ms total)
35: [ PASSED ] 69 tests.
35/54 Test #35: AnalysisDataUnitTests ............... Passed 0.32 sec
test 36
Start 36: CoordinateIOTests
36: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/coordinateio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/CoordinateIOTests.xml"
36: Test timeout computed to be: 30
36: [==========] Running 64 tests from 19 test cases.
36: [----------] Global test environment set-up.
36: [----------] 1 test from OutputSelectorDeathTest
36: [ RUN ] OutputSelectorDeathTest.RejectsBadSelection
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] OutputSelectorDeathTest.RejectsBadSelection (34 ms)
36: [----------] 1 test from OutputSelectorDeathTest (34 ms total)
36:
36: [----------] 5 tests from TrajectoryFrameWriterTest
36: [ RUN ] TrajectoryFrameWriterTest.RejectsWrongFiletype
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.RejectsWrongFiletype (23 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithPdbAndNoAtoms (22 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderFailsWithGroAndNoAtoms (22 ms)
36: [ RUN ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] TrajectoryFrameWriterTest.BuilderImplictlyAddsAtoms (44 ms)
36: [ RUN ] TrajectoryFrameWriterTest.TNGOutputWorks
36: [ OK ] TrajectoryFrameWriterTest.TNGOutputWorks (0 ms)
36: [----------] 5 tests from TrajectoryFrameWriterTest (113 ms total)
36:
36: [----------] 5 tests from OutputAdapterContainer
36: [ RUN ] OutputAdapterContainer.MakeEmpty
36: [ OK ] OutputAdapterContainer.MakeEmpty (0 ms)
36: [ RUN ] OutputAdapterContainer.AddAdapter
36: [ OK ] OutputAdapterContainer.AddAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectBadAdapter
36: [ OK ] OutputAdapterContainer.RejectBadAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.RejectDuplicateAdapter
36: [ OK ] OutputAdapterContainer.RejectDuplicateAdapter (0 ms)
36: [ RUN ] OutputAdapterContainer.AcceptMultipleAdapters
36: [ OK ] OutputAdapterContainer.AcceptMultipleAdapters (0 ms)
36: [----------] 5 tests from OutputAdapterContainer (1 ms total)
36:
36: [----------] 5 tests from FlagTest
36: [ RUN ] FlagTest.CanSetSimpleFlag
36: [ OK ] FlagTest.CanSetSimpleFlag (0 ms)
36: [ RUN ] FlagTest.CanAddNewBox
36: [ OK ] FlagTest.CanAddNewBox (0 ms)
36: [ RUN ] FlagTest.SetsImplicitPrecisionChange
36: [ OK ] FlagTest.SetsImplicitPrecisionChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitStartTimeChange
36: [ OK ] FlagTest.SetsImplicitStartTimeChange (0 ms)
36: [ RUN ] FlagTest.SetsImplicitTimeStepChange
36: [ OK ] FlagTest.SetsImplicitTimeStepChange (0 ms)
36: [----------] 5 tests from FlagTest (2 ms total)
36:
36: [----------] 5 tests from SetAtomsTest
36: [ RUN ] SetAtomsTest.RemovesExistingAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.RemovesExistingAtoms (23 ms)
36: [ RUN ] SetAtomsTest.AddsNewAtoms
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.AddsNewAtoms (22 ms)
36: [ RUN ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsOnRequiredAtomsNotAvailable (23 ms)
36: [ RUN ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.WillUseOldAtomsWhenNoNewAvailable (22 ms)
36: [ RUN ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] SetAtomsTest.ThrowsWhenUserAtomReplacementNotPossible (22 ms)
36: [----------] 5 tests from SetAtomsTest (113 ms total)
36:
36: [----------] 2 tests from SetBothTimeTest
36: [ RUN ] SetBothTimeTest.StartTimeZeroWorks
36: [ OK ] SetBothTimeTest.StartTimeZeroWorks (1 ms)
36: [ RUN ] SetBothTimeTest.SetStartTimeNonZeroWorks
36: [ OK ] SetBothTimeTest.SetStartTimeNonZeroWorks (0 ms)
36: [----------] 2 tests from SetBothTimeTest (1 ms total)
36:
36: [----------] 2 tests from SetStartTimeTest
36: [ RUN ] SetStartTimeTest.WorksWithNonZeroStart
36: [ OK ] SetStartTimeTest.WorksWithNonZeroStart (1 ms)
36: [ RUN ] SetStartTimeTest.WorksWithZeroStart
36: [ OK ] SetStartTimeTest.WorksWithZeroStart (0 ms)
36: [----------] 2 tests from SetStartTimeTest (1 ms total)
36:
36: [----------] 1 test from SetTimeStepTest
36: [ RUN ] SetTimeStepTest.SetTimeStepWorks
36: [ OK ] SetTimeStepTest.SetTimeStepWorks (0 ms)
36: [----------] 1 test from SetTimeStepTest (1 ms total)
36:
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/0 (22 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/1 (22 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/2 (22 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/3 (22 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/4 (22 ms)
36: [ RUN ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] CoordinateFileFileFormats/TrajectoryFrameWriterTest.WorksWithFormats/5 (22 ms)
36: [----------] 6 tests from CoordinateFileFileFormats/TrajectoryFrameWriterTest (135 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/0 (22 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/1 (22 ms)
36: [ RUN ] ModuleSupported/SetAtomsSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetAtomsSupportedFiles.Works/2 (22 ms)
36: [----------] 3 tests from ModuleSupported/SetAtomsSupportedFiles (67 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/1 (1 ms)
36: [ RUN ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetAtomsUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetAtomsUnSupportedFiles (1 ms total)
36:
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/0 (46 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/1 (46 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/2 (46 ms)
36: [ RUN ] ModuleSupported/AnyOutputSupportedFiles.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/AnyOutputSupportedFiles.Works/3 (46 ms)
36: [----------] 4 tests from ModuleSupported/AnyOutputSupportedFiles (185 ms total)
36:
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/0 (22 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/1 (23 ms)
36: [ RUN ] ModuleSupported/SetVelocitySupportedFiles.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetVelocitySupportedFiles.Works/2 (22 ms)
36: [----------] 3 tests from ModuleSupported/SetVelocitySupportedFiles (68 ms total)
36:
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetVelocityUnSupportedFiles.Works/2 (0 ms)
36: [----------] 3 tests from ModuleUnSupported/SetVelocityUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/0 (23 ms)
36: [ RUN ] ModuleSupported/SetForceSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetForceSupportedFiles.Works/1 (22 ms)
36: [----------] 2 tests from ModuleSupported/SetForceSupportedFiles (45 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetForceUnSupportedFiles.Works/3 (0 ms)
36: [----------] 4 tests from ModuleUnSupported/SetForceUnSupportedFiles (1 ms total)
36:
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/0 (22 ms)
36: [ RUN ] ModuleSupported/SetPrecisionSupportedFiles.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/SetPrecisionSupportedFiles.Works/1 (22 ms)
36: [----------] 2 tests from ModuleSupported/SetPrecisionSupportedFiles (45 ms total)
36:
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/0 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/1 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/2 (0 ms)
36: [ RUN ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3
36: [ OK ] ModuleUnSupported/SetPrecisionUnSupportedFiles.Works/3 (1 ms)
36: [----------] 4 tests from ModuleUnSupported/SetPrecisionUnSupportedFiles (2 ms total)
36:
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/0
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/0 (22 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/1
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/1 (22 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/2
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/2 (22 ms)
36: [ RUN ] ModuleSupported/NoOptionalOutput.Works/3
36:
36: WARNING: Masses and atomic (Van der Waals) radii will be guessed
36: based on residue and atom names, since they could not be
36: definitively assigned from the information in your input
36: files. These guessed numbers might deviate from the mass
36: and radius of the atom type. Please check the output
36: files if necessary.
36:
36: [ OK ] ModuleSupported/NoOptionalOutput.Works/3 (22 ms)
36: [----------] 4 tests from ModuleSupported/NoOptionalOutput (90 ms total)
36:
36: [----------] Global test environment tear-down
36: [==========] 64 tests from 19 test cases ran. (914 ms total)
36: [ PASSED ] 64 tests.
36/54 Test #36: CoordinateIOTests ................... Passed 0.99 sec
test 37
Start 37: TrajectoryAnalysisUnitTests
37: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/trajectoryanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/TrajectoryAnalysisUnitTests.xml"
37: Test timeout computed to be: 30
37: [==========] Running 82 tests from 16 test cases.
37: [----------] Global test environment set-up.
37: [----------] 5 tests from ClustsizeTest
37: [ RUN ] ClustsizeTest.NoMolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 2, cmax: 4, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolDefaultCutoff (13 ms)
37: [ RUN ] ClustsizeTest.NoMolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Group 0 ( SOL) has 24 elements
37: There is one group in the index
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 24
37: cmid: 1, cmax: 6, max_size: 6
37: 16% 33% 50% 66% 83%100%cmid: 6, cmax: 18, max_size: 6
37: 16% 33% 50% 66% 83%100%[ OK ] ClustsizeTest.NoMolShortCutoff (11 ms)
37: [ RUN ] ClustsizeTest.MolDefaultCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolDefaultCutoff (13 ms)
37: [ RUN ] ClustsizeTest.MolShortCutoff
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 1, cmax: 6, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolShortCutoff (12 ms)
37: [ RUN ] ClustsizeTest.MolCSize
37: Reading frames from pdb file
Reading frame 0 time 0.000 Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Total number of atoms in clusters = 8
37: cmid: 2, cmax: 4, max_size: 2
37: 50%100%cmid: 2, cmax: 6, max_size: 2
37: 50%100%[ OK ] ClustsizeTest.MolCSize (13 ms)
37: [----------] 5 tests from ClustsizeTest (64 ms total)
37:
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.WritesHelp (5 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.RunsWithSubsetTrajectory (16 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset
37: Reading frames from gro file 'Test system', 8 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.DetectsIncorrectTrajectorySubset (16 ms)
37: [ RUN ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory
37: [ OK ] TrajectoryAnalysisCommandLineRunnerTest.FailsWithTrajectorySubsetWithoutTrajectory (2 ms)
37: [----------] 4 tests from TrajectoryAnalysisCommandLineRunnerTest (39 ms total)
37:
37: [----------] 11 tests from AngleModuleTest
37: [ RUN ] AngleModuleTest.ComputesSimpleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesSimpleAngles (18 ms)
37: [ RUN ] AngleModuleTest.ComputesDihedrals
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesDihedrals (18 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPairAngles (18 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorPlanePairAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorPlanePairAngles (18 ms)
37: [ RUN ] AngleModuleTest.ComputesPlaneZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesPlaneZAxisAngles (17 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorSphereNormalZAxisAngles (18 ms)
37: [ RUN ] AngleModuleTest.ComputesVectorTimeZeroAngles
37: Reading frames from gro file 'Test system for different angles', 33 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesVectorTimeZeroAngles (20 ms)
37: [ RUN ] AngleModuleTest.ComputesMultipleAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.ComputesMultipleAngles (19 ms)
37: [ RUN ] AngleModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesDynamicSelections (17 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorAngles (18 ms)
37: [ RUN ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] AngleModuleTest.HandlesOneVsMultipleVectorGroupsAngles (19 ms)
37: [----------] 11 tests from AngleModuleTest (201 ms total)
37:
37: [----------] 4 tests from ConvertTrjModuleTest
37: [ RUN ] ConvertTrjModuleTest.WritesNormalOutput
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesNormalOutput (56 ms)
37: [ RUN ] ConvertTrjModuleTest.WritesAtomSubset
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WritesAtomSubset (62 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomAdding
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomAdding (8 ms)
37: [ RUN ] ConvertTrjModuleTest.WorksWithAtomsAndSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/clustsize.tpr, VERSION 2016 (single precision)
37: Reading frames from pdb file
Reading frame 0 time 0.000 '', 24 atoms
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37: [ OK ] ConvertTrjModuleTest.WorksWithAtomsAndSelection (9 ms)
37: [----------] 4 tests from ConvertTrjModuleTest (135 ms total)
37:
37: [----------] 3 tests from DistanceModuleTest
37: [ RUN ] DistanceModuleTest.ComputesDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: [ OK ] DistanceModuleTest.ComputesDistances (22 ms)
37: [ RUN ] DistanceModuleTest.ComputesMultipleDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2:
37: Number of samples: 5
37: Average distance: 1.43246 nm
37: Standard deviation: 0.96700 nm
37: resindex 1 to 4 and atomname CB merge resindex 2 to 5 and atomname CB:
37: Number of samples: 4
37: Average distance: 1.81066 nm
37: Standard deviation: 0.79289 nm
37: [ OK ] DistanceModuleTest.ComputesMultipleDistances (53 ms)
37: [ RUN ] DistanceModuleTest.HandlesDynamicSelections
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: atomname S1 S2 and res_cog x < 2.8:
37: Number of samples: 3
37: Average distance: 1.72076 nm
37: Standard deviation: 1.24839 nm
37: [ OK ] DistanceModuleTest.HandlesDynamicSelections (22 ms)
37: [----------] 3 tests from DistanceModuleTest (100 ms total)
37:
37: [----------] 2 tests from ExtractClusterModuleTest
37: [ RUN ] ExtractClusterModuleTest.WorksWithAllAtoms
37: trr version: GMX_trn_file (single precision)
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAllAtoms (17 ms)
37: [ RUN ] ExtractClusterModuleTest.WorksWithAtomSubset
37:
Reading frame 0 time 0.000
Reading frame 1 time 0.002
Reading frame 2 time 0.004
Reading frame 3 time 0.006
Reading frame 4 time 0.008
Reading frame 5 time 0.010
Reading frame 6 time 0.012
Reading frame 7 time 0.014
Reading frame 8 time 0.016
Reading frame 9 time 0.018
Reading frame 10 time 0.020
Reading frame 11 time 0.022
Reading frame 12 time 0.024
Reading frame 13 time 0.026
Reading frame 14 time 0.028
Reading frame 15 time 0.030
Reading frame 16 time 0.032
Reading frame 17 time 0.034
Reading frame 18 time 0.036
Reading frame 19 time 0.038
Reading frame 20 time 0.040
37: Analyzed 26 frames, last time 0.050
37: There are 8 clusters containing 26 structures, highest framenr is 25
37: [ OK ] ExtractClusterModuleTest.WorksWithAtomSubset (14 ms)
37: [----------] 2 tests from ExtractClusterModuleTest (32 ms total)
37:
37: [----------] 2 tests from FreeVolumeModuleTest
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolume
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for CO2-RM. Set to zero.
37: Could not determine VDW radius for 40 particles. These were set to zero.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 13
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.02 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1256 +/- 0.0000 nm^3
37: Fractional free volume 0.194 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolume (807 ms)
37: [ RUN ] FreeVolumeModuleTest.ComputesFreeVolumeSelection
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37: Reading file /<<PKGBUILDDIR>>/src/gromacs/trajectoryanalysis/tests/freevolume.tpr, VERSION 4.5.5 (single precision)
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: cutoff = 0.18 nm
37: probe_radius = 0 nm
37: seed = 17
37: ninsert = 1000 probes per nm^3
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Tuanan C. Lourenco and Mariny F. C. Coelho and Teodorico C. Ramalho and David
37: van der Spoel and Luciano T. Costa
37: Insights on the Solubility of CO2 in 1-Ethyl-3-methylimidazolium
37: Bis(trifluoromethylsulfonyl)imide from the Microscopic Point of View
37: Environ. Sci. Technol. 47 (2013) pp. 7421-7429
37: -------- -------- --- Thank You --- -------- --------
37:
37: Free volume 38.48 +/- 0.00 %
37: Total volume 68.92 +/- 0.00 nm^3
37: Number of molecules 340 total mass 63491.38 Dalton
37: Average molar mass: 186.74 Dalton
37: Density rho: 1529.71 +/- 0.00 nm^3
37: Molecular volume Vm assuming homogeneity: 0.2027 +/- 0.0000 nm^3
37: Molecular van der Waals volume assuming homogeneity: 0.1247 +/- 0.0000 nm^3
37: Fractional free volume 0.200 +/- 0.000
37: [ OK ] FreeVolumeModuleTest.ComputesFreeVolumeSelection (700 ms)
37: [----------] 2 tests from FreeVolumeModuleTest (1507 ms total)
37:
37: [----------] 9 tests from PairDistanceModuleTest
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistances
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistances (18 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesAllDistancesWithCutoff (17 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMinDistanceWithCutoff (17 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistance
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistance (17 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesMaxDistanceWithCutoff (17 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMinDistanceWithCutoff (17 ms)
37: [ RUN ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.ComputesGroupedMaxDistanceWithCutoff (18 ms)
37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwritten (17 ms)
37: [ RUN ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] PairDistanceModuleTest.CoordinateSelectionIsNotOverwrittenWithExplicitGroup (17 ms)
37: [----------] 9 tests from PairDistanceModuleTest (158 ms total)
37:
37: [----------] 5 tests from RdfModuleTest
37: [ RUN ] RdfModuleTest.BasicTest
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.BasicTest (151 ms)
37: [ RUN ] RdfModuleTest.SelectionsSolelyFromIndexFileWork
37: Reading frames from gro file '216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984', 648 atoms.
37:
Reading frame 0 time 0.000
Last frame 0 time 0.000
37: Analyzed 1 frames, last time 0.000
37: [ OK ] RdfModuleTest.SelectionsSolelyFromIndexFileWork (105 ms)
37: [ RUN ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.SelectionsFromBothTopologyFileAndIndexFileWork (153 ms)
37: [ RUN ] RdfModuleTest.CalculatesSurf
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesSurf (90 ms)
37: [ RUN ] RdfModuleTest.CalculatesXY
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] RdfModuleTest.CalculatesXY (178 ms)
37: [----------] 5 tests from RdfModuleTest (683 ms total)
37:
37: [----------] 5 tests from SasaModuleTest
37: [ RUN ] SasaModuleTest.BasicTest
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.BasicTest (116 ms)
37: [ RUN ] SasaModuleTest.HandlesSelectedResidues
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesSelectedResidues (51 ms)
37: [ RUN ] SasaModuleTest.WritesConnollySurfaceWithSolute
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.WritesConnollySurfaceWithSolute (45 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicOutputGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicOutputGroup (60 ms)
37: [ RUN ] SasaModuleTest.HandlesDynamicCalculationGroup
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: Frank Eisenhaber and Philip Lijnzaad and Patrick Argos and Chris Sander and
37: Michael Scharf
37: The Double Cube Lattice Method: Efficient Approaches to Numerical Integration
37: of Surface Area and Volume and to Dot Surface Contouring of Molecular
37: Assemblies
37: J. Comp. Chem. 16 (1995) pp. 273-284
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: NOTE: From version 5.0 trajectoryanalysis-test uses the Van der Waals radii
37: from the source below. This means the results may be different
37: compared to previous GROMACS versions.
37:
37: ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++
37: A. Bondi
37: van der Waals Volumes and Radii
37: J. Phys. Chem. 68 (1964) pp. 441-451
37: -------- -------- --- Thank You --- -------- --------
37:
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37: [ OK ] SasaModuleTest.HandlesDynamicCalculationGroup (58 ms)
37: [----------] 5 tests from SasaModuleTest (346 ms total)
37:
37: [----------] 8 tests from SelectModuleTest
37: [ RUN ] SelectModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.BasicTest (46 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithNonPDBInput (25 ms)
37: [ RUN ] SelectModuleTest.HandlesPDBOutputWithPDBInput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesPDBOutputWithPDBInput (24 ms)
37: [ RUN ] SelectModuleTest.HandlesMaxPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesMaxPDBOutput (24 ms)
37: [ RUN ] SelectModuleTest.HandlesSelectedPDBOutput
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.HandlesSelectedPDBOutput (24 ms)
37: [ RUN ] SelectModuleTest.NormalizesSizes
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.NormalizesSizes (17 ms)
37: [ RUN ] SelectModuleTest.WritesResidueNumbers
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueNumbers (16 ms)
37: [ RUN ] SelectModuleTest.WritesResidueIndices
37:
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37: Analyzed topology coordinates
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] SelectModuleTest.WritesResidueIndices (17 ms)
37: [----------] 8 tests from SelectModuleTest (198 ms total)
37:
37: [----------] 10 tests from SurfaceAreaTest
37: [ RUN ] SurfaceAreaTest.ComputesSinglePoint
37: [ OK ] SurfaceAreaTest.ComputesSinglePoint (0 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPoints
37: [ OK ] SurfaceAreaTest.ComputesTwoPoints (7 ms)
37: [ RUN ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius
37: [ OK ] SurfaceAreaTest.ComputesTwoPointsOfUnequalRadius (7 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints12
37: [ OK ] SurfaceAreaTest.SurfacePoints12 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints32
37: [ OK ] SurfaceAreaTest.SurfacePoints32 (1 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints42
37: [ OK ] SurfaceAreaTest.SurfacePoints42 (2 ms)
37: [ RUN ] SurfaceAreaTest.SurfacePoints122
37: [ OK ] SurfaceAreaTest.SurfacePoints122 (6 ms)
37: [ RUN ] SurfaceAreaTest.Computes100Points
37: [ OK ] SurfaceAreaTest.Computes100Points (4 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithRectangularPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithRectangularPBC (14 ms)
37: [ RUN ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC
37: [ OK ] SurfaceAreaTest.Computes100PointsWithTriclinicPBC (17 ms)
37: [----------] 10 tests from SurfaceAreaTest (63 ms total)
37:
37: [----------] 4 tests from TopologyInformation
37: [ RUN ] TopologyInformation.CantWorkWithoutReadingAFile
37: [ OK ] TopologyInformation.CantWorkWithoutReadingAFile (0 ms)
37: [ RUN ] TopologyInformation.WorksWithGroFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithGroFile (24 ms)
37: [ RUN ] TopologyInformation.WorksWithPdbFile
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TopologyInformation.WorksWithPdbFile (22 ms)
37: [ RUN ] TopologyInformation.WorksWithTprFromPdbFile
37:
37: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: For a correct single-point energy evaluation with nsteps = 0, use
37: continuation = yes to avoid constraining the input coordinates.
37:
37: Setting the LD random seed to -1949570561
37: Generated 330891 of the 330891 non-bonded parameter combinations
37: Generating 1-4 interactions: fudge = 0.5
37: Generated 330891 of the 330891 1-4 parameter combinations
37: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
37:
37: NOTE 2 [file lysozyme.top, line 1465]:
37: System has non-zero total charge: 2.000000
37: Total charge should normally be an integer. See
37: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
37: for discussion on how close it should be to an integer.
37:
37:
37:
37: Number of degrees of freedom in T-Coupling group rest is 465.00
37:
37: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: NVE simulation with an initial temperature of zero: will use a Verlet
37: buffer of 10%. Check your energy drift!
37:
37:
37: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.mdp]:
37: You are using a plain Coulomb cut-off, which might produce artifacts.
37: You might want to consider using PME electrostatics.
37:
37:
37:
37: There were 4 notes
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
37: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/trajectoryanalysis/tests/Testing/Temporary/TopologyInformation_WorksWithTprFromPdbFile_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
37: Analysing residue names:
37: There are: 10 Protein residues
37: Analysing Protein...
37: This run will generate roughly 0 Mb of data
37: [ OK ] TopologyInformation.WorksWithTprFromPdbFile (4823 ms)
37: [----------] 4 tests from TopologyInformation (4869 ms total)
37:
37: [----------] 4 tests from TrajectoryModuleTest
37: [ RUN ] TrajectoryModuleTest.BasicTest
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.BasicTest (20 ms)
37: [ RUN ] TrajectoryModuleTest.PlotsXOnly
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.PlotsXOnly (20 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoVelocities
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoVelocities (35 ms)
37: [ RUN ] TrajectoryModuleTest.HandlesNoForces
37: Reading frames from gro file 'Test system', 15 atoms.
37:
Reading frame 0 time 0.000
37: WARNING: If there are molecules in the input trajectory file
37: that are broken across periodic boundaries, they
37: cannot be made whole (or treated as whole) without
37: you providing a run input file.
37:
37:
Reading frame 1 time 0.000
Last frame 1 time 0.000
37: Analyzed 2 frames, last time 0.000
37:
37: WARNING: Masses and atomic (Van der Waals) radii will be guessed
37: based on residue and atom names, since they could not be
37: definitively assigned from the information in your input
37: files. These guessed numbers might deviate from the mass
37: and radius of the atom type. Please check the output
37: files if necessary.
37:
37: [ OK ] TrajectoryModuleTest.HandlesNoForces (18 ms)
37: [----------] 4 tests from TrajectoryModuleTest (93 ms total)
37:
37: [----------] 5 tests from UnionFinderTest
37: [ RUN ] UnionFinderTest.WorksEmpty
37: [ OK ] UnionFinderTest.WorksEmpty (1 ms)
37: [ RUN ] UnionFinderTest.BasicMerges
37: [ OK ] UnionFinderTest.BasicMerges (0 ms)
37: [ RUN ] UnionFinderTest.LargerMerges
37: [ OK ] UnionFinderTest.LargerMerges (0 ms)
37: [ RUN ] UnionFinderTest.LongRightMerge
37: [ OK ] UnionFinderTest.LongRightMerge (0 ms)
37: [ RUN ] UnionFinderTest.LongLeftMerge
37: [ OK ] UnionFinderTest.LongLeftMerge (0 ms)
37: [----------] 5 tests from UnionFinderTest (1 ms total)
37:
37: [----------] 1 test from MappedUnionFinderTest
37: [ RUN ] MappedUnionFinderTest.BasicMerges
37: [ OK ] MappedUnionFinderTest.BasicMerges (0 ms)
37: [----------] 1 test from MappedUnionFinderTest (0 ms total)
37:
37: [----------] Global test environment tear-down
37: [==========] 82 tests from 16 test cases ran. (8489 ms total)
37: [ PASSED ] 82 tests.
37/54 Test #37: TrajectoryAnalysisUnitTests ......... Passed 8.57 sec
test 38
Start 38: EnergyAnalysisUnitTests
38: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/energyanalysis-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/EnergyAnalysisUnitTests.xml"
38: Test timeout computed to be: 30
38: [==========] Running 7 tests from 4 test cases.
38: [----------] Global test environment set-up.
38: [----------] 1 test from DhdlTest
38: [ RUN ] DhdlTest.ExtractDhdl
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.edr as double precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/dhdl.tpr, VERSION 2016-dev-20160810-e3ded7f (double precision)
38: Note: file tpx version 110, software tpx version 119
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.010
Reading energy frame 2 time 0.020
Reading energy frame 3 time 0.030
Reading energy frame 4 time 0.040
Reading energy frame 5 time 0.050
Reading energy frame 6 time 0.060
Reading energy frame 7 time 0.070
Reading energy frame 8 time 0.080
Reading energy frame 9 time 0.090
Reading energy frame 10 time 0.100
Reading energy frame 11 time 0.110
Reading energy frame 12 time 0.120
Reading energy frame 13 time 0.130
Reading energy frame 14 time 0.140
Reading energy frame 15 time 0.150
Reading energy frame 16 time 0.160
Reading energy frame 17 time 0.170
Reading energy frame 18 time 0.180
Reading energy frame 19 time 0.190
Reading energy frame 20 time 0.200
Reading energy frame 30 time 0.300
Reading energy frame 40 time 0.400
Reading energy frame 50 time 0.500
Reading energy frame 60 time 0.600
Reading energy frame 70 time 0.700
Reading energy frame 80 time 0.800
Reading energy frame 90 time 0.900
Reading energy frame 100 time 1.000
Last energy frame read 100 time 1.000
38:
38:
38: Wrote 8 lambda values with 101 samples as 808 dH data blocks to /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/energyanalysis/tests/Testing/Temporary/DhdlTest_ExtractDhdl_dhdl.xvg
38: [ OK ] DhdlTest.ExtractDhdl (95 ms)
38: [----------] 1 test from DhdlTest (98 ms total)
38:
38: [----------] 1 test from OriresTest
38: [ RUN ] OriresTest.ExtractOrires
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.edr as single precision energy file
38: Reading file /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/orires.tpr, VERSION 2017-dev-20170725-fea8651 (single precision)
38: Note: file tpx version 111, software tpx version 119
38: Found 7 orientation restraints with 1 experimentsSelect the orientation restraint labels you want (-1 is all)
38: End your selection with 0
38: Selecting all 7 orientation restraints
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Reading energy frame 2 time 0.004
Reading energy frame 3 time 0.006
Reading energy frame 4 time 0.008
Reading energy frame 5 time 0.010
Reading energy frame 6 time 0.012
Reading energy frame 7 time 0.014
Reading energy frame 8 time 0.016
Reading energy frame 9 time 0.018
Reading energy frame 10 time 0.020
Last energy frame read 10 time 0.020
38: [ OK ] OriresTest.ExtractOrires (105 ms)
38: [----------] 1 test from OriresTest (106 ms total)
38:
38: [----------] 3 tests from EnergyTest
38: [ RUN ] EnergyTest.ExtractEnergy
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Potential -34142.2 39 228.993 -62.8906 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: [ OK ] EnergyTest.ExtractEnergy (16 ms)
38: [ RUN ] EnergyTest.ExtractEnergyByNumber
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 3 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Coul. recip. 302.771 2.8 17.5152 12.5403 (kJ/mol)
38: Kinetic En. 6132.38 0.42 119.428 -0.266996 (kJ/mol)
38: Pres. DC -268.49 3 8.52175 13.2804 (bar)
38: [ OK ] EnergyTest.ExtractEnergyByNumber (16 ms)
38: [ RUN ] EnergyTest.ExtractEnergyMixed
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
38: Select the terms you want from the following list by
38: selecting either (part of) the name or the number or a combination.
38: End your selection with an empty line or a zero.
38: -------------------------------------------------------------------
38: 1 LJ-(SR) 2 Disper.-corr. 3 Coulomb-(SR) 4 Coul.-recip.
38: 5 Potential 6 Kinetic-En. 7 Total-Energy 8 Temperature
38: 9 Pres.-DC 10 Pressure 11 Box-X 12 Box-Y
38: 13 Box-Z 14 Volume 15 Density 16 pV
38: 17 Enthalpy 18 Vir-XX 19 Vir-XY 20 Vir-XZ
38: 21 Vir-YX 22 Vir-YY 23 Vir-YZ 24 Vir-ZX
38: 25 Vir-ZY 26 Vir-ZZ 27 Pres-XX 28 Pres-XY
38: 29 Pres-XZ 30 Pres-YX 31 Pres-YY 32 Pres-YZ
38: 33 Pres-ZX 34 Pres-ZY 35 Pres-ZZ 36 #Surf*SurfTen
38: 37 Box-Vel-XX 38 Box-Vel-YY 39 Box-Vel-ZZ 40 T-System
38:
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 4 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Total Energy -28009.8 39 258.637 -63.1577 (kJ/mol)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: Box-Z 2.92457 0.0054 0.0151558 0.0234974 (nm)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: [ OK ] EnergyTest.ExtractEnergyMixed (32 ms)
38: [----------] 3 tests from EnergyTest (66 ms total)
38:
38: [----------] 2 tests from ViscosityTest
38: [ RUN ] ViscosityTest.EinsteinViscosity
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosity (54 ms)
38: [ RUN ] ViscosityTest.EinsteinViscosityIntegral
38: Opened /<<PKGBUILDDIR>>/src/gromacs/energyanalysis/tests/ener.edr as single precision energy file
38:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.200
Reading energy frame 2 time 0.400
Reading energy frame 3 time 0.600
Reading energy frame 4 time 0.800
Reading energy frame 5 time 1.000
Reading energy frame 6 time 1.200
Reading energy frame 7 time 1.400
Reading energy frame 8 time 1.600
Reading energy frame 9 time 1.800
Reading energy frame 10 time 2.000
Reading energy frame 11 time 2.200
Reading energy frame 12 time 2.400
Reading energy frame 13 time 2.600
Reading energy frame 14 time 2.800
Reading energy frame 15 time 3.000
Reading energy frame 16 time 3.200
Reading energy frame 17 time 3.400
Reading energy frame 18 time 3.600
Reading energy frame 19 time 3.800
Reading energy frame 20 time 4.000
Reading energy frame 30 time 6.000
Reading energy frame 40 time 8.000
Reading energy frame 50 time 10.000
Last energy frame read 50 time 10.000
38:
38: Statistics over 5001 steps [ 0.0000 through 10.0000 ps ], 12 data sets
38: All statistics are over 5001 points
38:
38: Energy Average Err.Est. RMSD Tot-Drift
38: -------------------------------------------------------------------------------
38: Pres-XX 20.2092 65 717.193 185.978 (bar)
38: Pres-XY -47.7351 39 372.522 207.456 (bar)
38: Pres-XZ 11.477 31 379.79 6.80818 (bar)
38: Pres-YX -47.7106 39 372.525 207.5 (bar)
38: Pres-YY 38.9241 40 803.899 -27.1505 (bar)
38: Pres-YZ -41.3534 45 401.216 114.663 (bar)
38: Pres-ZX 11.5238 31 379.804 6.91707 (bar)
38: Pres-ZY -41.3119 45 401.196 114.743 (bar)
38: Pres-ZZ -43.1021 63 748.522 -173.491 (bar)
38: Temperature 300.001 0.02 5.8425 -0.0130558 (K)
38: Volume 25.0162 0.14 0.386769 0.598615 (nm^3)
38: Pressure 5.34371 4.1 605.307 -4.88771 (bar)
38: [ OK ] ViscosityTest.EinsteinViscosityIntegral (63 ms)
38: [----------] 2 tests from ViscosityTest (119 ms total)
38:
38: [----------] Global test environment tear-down
38: [==========] 7 tests from 4 test cases ran. (390 ms total)
38: [ PASSED ] 7 tests.
38/54 Test #38: EnergyAnalysisUnitTests ............. Passed 0.45 sec
test 39
Start 39: ToolUnitTests
39: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/tool-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/ToolUnitTests.xml"
39: Test timeout computed to be: 30
39: [==========] Running 18 tests from 4 test cases.
39: [----------] Global test environment set-up.
39: [----------] 2 tests from DumpTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -38416394
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] DumpTest.WorksWithTpr
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
39: /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr:
39: inputrec:
39: integrator = md
39: tinit = 0
39: dt = 0.001
39: nsteps = 0
39: init-step = 0
39: simulation-part = 1
39: comm-mode = Linear
39: nstcomm = 100
39: bd-fric = 0
39: ld-seed = -38416394
39: emtol = 10
39: emstep = 0.01
39: niter = 20
39: fcstep = 0
39: nstcgsteep = 1000
39: nbfgscorr = 10
39: rtpi = 0.05
39: nstxout = 0
39: nstvout = 0
39: nstfout = 0
39: nstlog = 1000
39: nstcalcenergy = 100
39: nstenergy = 1000
39: nstxout-compressed = 0
39: compressed-x-precision = 1000
39: cutoff-scheme = Verlet
39: nstlist = 10
39: pbc = xyz
39: periodic-molecules = false
39: verlet-buffer-tolerance = -1
39: rlist = 1.1
39: coulombtype = Cut-off
39: coulomb-modifier = Potential-shift
39: rcoulomb-switch = 0
39: rcoulomb = 1
39: epsilon-r = 1
39: epsilon-rf = inf
39: vdw-type = Cut-off
39: vdw-modifier = Potential-shift
39: rvdw-switch = 0
39: rvdw = 1
39: DispCorr = No
39: table-extension = 1
39: fourierspacing = 0.12
39: fourier-nx = 0
39: fourier-ny = 0
39: fourier-nz = 0
39: pme-order = 4
39: ewald-rtol = 1e-05
39: ewald-rtol-lj = 0.001
39: lj-pme-comb-rule = Geometric
39: ewald-geometry = 0
39: epsilon-surface = 0
39: tcoupl = No
39: nsttcouple = -1
39: nh-chain-length = 0
39: print-nose-hoover-chain-variables = false
39: pcoupl = No
39: pcoupltype = Isotropic
39: nstpcouple = -1
39: tau-p = 1
39: compressibility (3x3):
39: compressibility[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: compressibility[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p (3x3):
39: ref-p[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: ref-p[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: refcoord-scaling = No
39: posres-com (3):
39: posres-com[0]= 0.00000e+00
39: posres-com[1]= 0.00000e+00
39: posres-com[2]= 0.00000e+00
39: posres-comB (3):
39: posres-comB[0]= 0.00000e+00
39: posres-comB[1]= 0.00000e+00
39: posres-comB[2]= 0.00000e+00
39: QMMM = false
39: QMconstraints = 0
39: QMMMscheme = 0
39: MMChargeScaleFactor = 1
39: qm-opts:
39: ngQM = 0
39: constraint-algorithm = Lincs
39: continuation = false
39: Shake-SOR = false
39: shake-tol = 0.0001
39: lincs-order = 4
39: lincs-iter = 1
39: lincs-warnangle = 30
39: nwall = 0
39: wall-type = 9-3
39: wall-r-linpot = -1
39: wall-atomtype[0] = -1
39: wall-atomtype[1] = -1
39: wall-density[0] = 0
39: wall-density[1] = 0
39: wall-ewald-zfac = 3
39: pull = false
39: awh = false
39: rotation = false
39: interactiveMD = false
39: disre = No
39: disre-weighting = Conservative
39: disre-mixed = false
39: dr-fc = 1000
39: dr-tau = 0
39: nstdisreout = 100
39: orire-fc = 0
39: orire-tau = 0
39: nstorireout = 100
39: free-energy = no
39: cos-acceleration = 0
39: deform (3x3):
39: deform[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: deform[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: simulated-tempering = false
39: swapcoords = no
39: userint1 = 0
39: userint2 = 0
39: userint3 = 0
39: userint4 = 0
39: userreal1 = 0
39: userreal2 = 0
39: userreal3 = 0
39: userreal4 = 0
39: applied-forces:
39: electric-field:
39: x:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: y:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: z:
39: E0 = 0
39: omega = 0
39: t0 = 0
39: sigma = 0
39: density-guided-simulation:
39: active = false
39: group = protein
39: similarity-measure = inner-product
39: atom-spreading-weight = unity
39: force-constant = 1e+09
39: gaussian-transform-spreading-width = 0.2
39: gaussian-transform-spreading-range-in-multiples-of-width = 4
39: reference-density-filename = reference.mrc
39: nst = 1
39: normalize-densities = true
39: adaptive-force-scaling = false
39: adaptive-force-scaling-time-constant = 4
39: grpopts:
39: nrdf: 465
39: ref-t: 0
39: tau-t: 0
39: annealing: No
39: annealing-npoints: 0
39: acc: 0 0 0
39: nfreeze: N N N
39: energygrp-flags[ 0]: 0
39: header:
39: bIr = present
39: bBox = present
39: bTop = present
39: bX = present
39: bV = present
39: bF = not present
39: natoms = 156
39: lambda = 0.000000e+00
39: buffer size = 70122
39: topology:
39: name="First 10 residues from 1AKI"
39: #atoms = 156
39: #molblock = 1
39: molblock (0):
39: moltype = 0 "Protein_chain_B"
39: #molecules = 1
39: #posres_xA = 0
39: #posres_xB = 0
39: bIntermolecularInteractions = false
39: ffparams:
39: atnr=10
39: ntypes=212
39: functype[0]=LJ_SR, c6= 3.35274678e-03, c12= 3.95094442e-06
39: functype[1]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[2]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
39: functype[3]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
39: functype[4]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
39: functype[5]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
39: functype[6]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
39: functype[7]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
39: functype[8]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
39: functype[9]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
39: functype[10]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[11]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[12]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[13]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[14]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[15]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[16]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[17]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[18]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[19]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[20]=LJ_SR, c6= 2.60916961e-03, c12= 3.84022374e-06
39: functype[21]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[22]=LJ_SR, c6= 2.03050409e-03, c12= 3.73260587e-06
39: functype[23]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
39: functype[24]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
39: functype[25]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
39: functype[26]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
39: functype[27]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
39: functype[28]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
39: functype[29]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
39: functype[30]=LJ_SR, c6= 6.41072082e-04, c12= 3.43856290e-07
39: functype[31]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[32]=LJ_SR, c6= 4.98894161e-04, c12= 3.34220112e-07
39: functype[33]=LJ_SR, c6= 1.22578125e-04, c12= 2.99263000e-08
39: functype[34]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
39: functype[35]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
39: functype[36]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
39: functype[37]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
39: functype[38]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
39: functype[39]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
39: functype[40]=LJ_SR, c6= 4.04775915e-03, c12= 7.32754594e-06
39: functype[41]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[42]=LJ_SR, c6= 3.15004110e-03, c12= 7.12219987e-06
39: functype[43]=LJ_SR, c6= 7.73964023e-04, c12= 6.37726703e-07
39: functype[44]=LJ_SR, c6= 4.88684509e-03, c12= 1.35898974e-05
39: functype[45]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
39: functype[46]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
39: functype[47]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
39: functype[48]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
39: functype[49]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
39: functype[50]=LJ_SR, c6= 2.81521126e-03, c12= 2.50631820e-06
39: functype[51]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[52]=LJ_SR, c6= 2.19084952e-03, c12= 2.43608151e-06
39: functype[53]=LJ_SR, c6= 5.38290978e-04, c12= 2.18128423e-07
39: functype[54]=LJ_SR, c6= 3.39879445e-03, c12= 4.64829665e-06
39: functype[55]=LJ_SR, c6= 2.36385715e-03, c12= 1.58990617e-06
39: functype[56]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
39: functype[57]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
39: functype[58]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
39: functype[59]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
39: functype[60]=LJ_SR, c6= 2.80388560e-03, c12= 4.30621225e-06
39: functype[61]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[62]=LJ_SR, c6= 2.18203568e-03, c12= 4.18553559e-06
39: functype[63]=LJ_SR, c6= 5.36125420e-04, c12= 3.74775753e-07
39: functype[64]=LJ_SR, c6= 3.38512102e-03, c12= 7.98643684e-06
39: functype[65]=LJ_SR, c6= 2.35434729e-03, c12= 2.73168564e-06
39: functype[66]=LJ_SR, c6= 2.34487570e-03, c12= 4.69342567e-06
39: functype[67]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
39: functype[68]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
39: functype[69]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
39: functype[70]=LJ_SR, c6= 5.81477529e-04, c12= 2.82897505e-07
39: functype[71]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[72]=LJ_SR, c6= 4.52516577e-04, c12= 2.74969627e-07
39: functype[73]=LJ_SR, c6= 1.11183168e-04, c12= 2.46209706e-08
39: functype[74]=LJ_SR, c6= 7.02015733e-04, c12= 5.24670621e-07
39: functype[75]=LJ_SR, c6= 4.88251036e-04, c12= 1.79458653e-07
39: functype[76]=LJ_SR, c6= 4.86286790e-04, c12= 3.08335570e-07
39: functype[77]=LJ_SR, c6= 1.00847496e-04, c12= 2.02561691e-08
39: functype[78]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
39: functype[79]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
39: functype[80]=LJ_SR, c6= 6.03335344e-04, c12= 2.35915461e-07
39: functype[81]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[82]=LJ_SR, c6= 4.69526733e-04, c12= 2.29304201e-07
39: functype[83]=LJ_SR, c6= 1.15362558e-04, c12= 2.05320568e-08
39: functype[84]=LJ_SR, c6= 7.28404594e-04, c12= 4.37536244e-07
39: functype[85]=LJ_SR, c6= 5.06604455e-04, c12= 1.49655159e-07
39: functype[86]=LJ_SR, c6= 5.04566372e-04, c12= 2.57128914e-07
39: functype[87]=LJ_SR, c6= 1.04638366e-04, c12= 1.68921372e-08
39: functype[88]=LJ_SR, c6= 1.08571736e-04, c12= 1.40867851e-08
39: functype[89]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
39: functype[90]=LJ_SR, c6= 7.20490366e-03, c12= 1.15394674e-05
39: functype[91]=LJ_SR, c6= 0.00000000e+00, c12= 0.00000000e+00
39: functype[92]=LJ_SR, c6= 5.60698940e-03, c12= 1.12160870e-05
39: functype[93]=LJ_SR, c6= 1.37763538e-03, c12= 1.00429619e-06
39: functype[94]=LJ_SR, c6= 8.69845432e-03, c12= 2.14014596e-05
39: functype[95]=LJ_SR, c6= 6.04976375e-03, c12= 7.32016804e-06
39: functype[96]=LJ_SR, c6= 6.02542540e-03, c12= 1.25770931e-05
39: functype[97]=LJ_SR, c6= 1.24956934e-03, c12= 8.26254733e-07
39: functype[98]=LJ_SR, c6= 1.29654081e-03, c12= 6.89034944e-07
39: functype[99]=LJ_SR, c6= 1.54830174e-02, c12= 3.37031588e-05
39: functype[100]=BONDS, b0A= 1.01000e-01, cbA= 3.63171e+05, b0B= 1.01000e-01, cbB= 3.63171e+05
39: functype[101]=BONDS, b0A= 1.47100e-01, cbA= 3.07106e+05, b0B= 1.47100e-01, cbB= 3.07106e+05
39: functype[102]=BONDS, b0A= 1.09000e-01, cbA= 2.84512e+05, b0B= 1.09000e-01, cbB= 2.84512e+05
39: functype[103]=BONDS, b0A= 1.52900e-01, cbA= 2.24262e+05, b0B= 1.52900e-01, cbB= 2.24262e+05
39: functype[104]=BONDS, b0A= 1.52200e-01, cbA= 2.65266e+05, b0B= 1.52200e-01, cbB= 2.65266e+05
39: functype[105]=BONDS, b0A= 1.22900e-01, cbA= 4.76976e+05, b0B= 1.22900e-01, cbB= 4.76976e+05
39: functype[106]=BONDS, b0A= 1.33500e-01, cbA= 4.10032e+05, b0B= 1.33500e-01, cbB= 4.10032e+05
39: functype[107]=BONDS, b0A= 1.44900e-01, cbA= 2.82002e+05, b0B= 1.44900e-01, cbB= 2.82002e+05
39: functype[108]=BONDS, b0A= 1.51000e-01, cbA= 2.65266e+05, b0B= 1.51000e-01, cbB= 2.65266e+05
39: functype[109]=BONDS, b0A= 1.40000e-01, cbA= 3.92459e+05, b0B= 1.40000e-01, cbB= 3.92459e+05
39: functype[110]=BONDS, b0A= 1.08000e-01, cbA= 3.07106e+05, b0B= 1.08000e-01, cbB= 3.07106e+05
39: functype[111]=BONDS, b0A= 1.46300e-01, cbA= 2.82002e+05, b0B= 1.46300e-01, cbB= 2.82002e+05
39: functype[112]=BONDS, b0A= 1.34000e-01, cbA= 4.02501e+05, b0B= 1.34000e-01, cbB= 4.02501e+05
39: functype[113]=BONDS, b0A= 1.81000e-01, cbA= 1.85770e+05, b0B= 1.81000e-01, cbB= 1.85770e+05
39: functype[114]=BONDS, b0A= 1.33600e-01, cbA= 2.29283e+05, b0B= 1.33600e-01, cbB= 2.29283e+05
39: functype[115]=BONDS, b0A= 1.25000e-01, cbA= 5.48941e+05, b0B= 1.25000e-01, cbB= 5.48941e+05
39: functype[116]=ANGLES, thA= 1.09500e+02, ctA= 2.92880e+02, thB= 1.09500e+02, ctB= 2.92880e+02
39: functype[117]=ANGLES, thA= 1.11200e+02, ctA= 6.69440e+02, thB= 1.11200e+02, ctB= 6.69440e+02
39: functype[118]=ANGLES, thA= 1.10700e+02, ctA= 3.13800e+02, thB= 1.10700e+02, ctB= 3.13800e+02
39: functype[119]=ANGLES, thA= 1.11100e+02, ctA= 5.27184e+02, thB= 1.11100e+02, ctB= 5.27184e+02
39: functype[120]=ANGLES, thA= 1.12700e+02, ctA= 4.88273e+02, thB= 1.12700e+02, ctB= 4.88273e+02
39: functype[121]=ANGLES, thA= 1.07800e+02, ctA= 2.76144e+02, thB= 1.07800e+02, ctB= 2.76144e+02
39: functype[122]=ANGLES, thA= 1.20400e+02, ctA= 6.69440e+02, thB= 1.20400e+02, ctB= 6.69440e+02
39: functype[123]=ANGLES, thA= 1.16600e+02, ctA= 5.85760e+02, thB= 1.16600e+02, ctB= 5.85760e+02
39: functype[124]=ANGLES, thA= 1.22900e+02, ctA= 6.69440e+02, thB= 1.22900e+02, ctB= 6.69440e+02
39: functype[125]=ANGLES, thA= 1.19800e+02, ctA= 2.92880e+02, thB= 1.19800e+02, ctB= 2.92880e+02
39: functype[126]=ANGLES, thA= 1.21900e+02, ctA= 4.18400e+02, thB= 1.21900e+02, ctB= 4.18400e+02
39: functype[127]=ANGLES, thA= 1.18400e+02, ctA= 3.17984e+02, thB= 1.18400e+02, ctB= 3.17984e+02
39: functype[128]=ANGLES, thA= 1.09700e+02, ctA= 6.69440e+02, thB= 1.09700e+02, ctB= 6.69440e+02
39: functype[129]=ANGLES, thA= 1.10100e+02, ctA= 5.27184e+02, thB= 1.10100e+02, ctB= 5.27184e+02
39: functype[130]=ANGLES, thA= 1.14000e+02, ctA= 5.27184e+02, thB= 1.14000e+02, ctB= 5.27184e+02
39: functype[131]=ANGLES, thA= 1.20000e+02, ctA= 5.85760e+02, thB= 1.20000e+02, ctB= 5.85760e+02
39: functype[132]=ANGLES, thA= 1.20000e+02, ctA= 5.27184e+02, thB= 1.20000e+02, ctB= 5.27184e+02
39: functype[133]=ANGLES, thA= 1.20000e+02, ctA= 2.92880e+02, thB= 1.20000e+02, ctB= 2.92880e+02
39: functype[134]=ANGLES, thA= 1.18400e+02, ctA= 2.92880e+02, thB= 1.18400e+02, ctB= 2.92880e+02
39: functype[135]=ANGLES, thA= 1.23200e+02, ctA= 4.18400e+02, thB= 1.23200e+02, ctB= 4.18400e+02
39: functype[136]=ANGLES, thA= 1.08600e+02, ctA= 4.18400e+02, thB= 1.08600e+02, ctB= 4.18400e+02
39: functype[137]=ANGLES, thA= 9.60000e+01, ctA= 3.68192e+02, thB= 9.60000e+01, ctB= 3.68192e+02
39: functype[138]=ANGLES, thA= 1.17000e+02, ctA= 5.85760e+02, thB= 1.17000e+02, ctB= 5.85760e+02
39: functype[139]=ANGLES, thA= 1.26000e+02, ctA= 6.69440e+02, thB= 1.26000e+02, ctB= 6.69440e+02
39: functype[140]=PDIHS, phiA= 1.80000000e+02, cpA= 4.39320000e+01, phiB= 1.80000000e+02, cpB= 4.39320000e+01, mult=2
39: functype[141]=PDIHS, phiA= 1.80000000e+02, cpA= 4.18400000e+00, phiB= 1.80000000e+02, cpB= 4.18400000e+00, mult=2
39: functype[142]=PDIHS, phiA= 1.80000000e+02, cpA= 4.60240000e+00, phiB= 1.80000000e+02, cpB= 4.60240000e+00, mult=2
39: functype[143]=RBDIHS, rbcA[0]= 5.46010000e-01, rbcA[1]= 1.63803000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.18405000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.46010000e-01, rbcB[1]= 1.63803000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.18405000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[144]=RBDIHS, rbcA[0]= 7.25920000e-01, rbcA[1]= 2.17777000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.90370000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 7.25920000e-01, rbcB[1]= 2.17777000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.90370000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[145]=RBDIHS, rbcA[0]= 1.27612000e+00, rbcA[1]= 1.16734000e+00, rbcA[2]= 8.95380000e-01, rbcA[3]=-3.33884000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.27612000e+00, rbcB[1]= 1.16734000e+00, rbcB[2]= 8.95380000e-01, rbcB[3]=-3.33884000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[146]=RBDIHS, rbcA[0]=-6.91824000e+00, rbcA[1]= 4.67562000e+00, rbcA[2]= 2.24262000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-6.91824000e+00, rbcB[1]= 4.67562000e+00, rbcB[2]= 2.24262000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[147]=RBDIHS, rbcA[0]= 9.70690000e-01, rbcA[1]= 2.91206000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.88275000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.70690000e-01, rbcB[1]= 2.91206000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.88275000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[148]=RBDIHS, rbcA[0]= 6.27600000e-01, rbcA[1]= 1.88280000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-2.51040000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 6.27600000e-01, rbcB[1]= 1.88280000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-2.51040000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[149]=RBDIHS, rbcA[0]=-1.58990000e-01, rbcA[1]=-4.76980000e-01, rbcA[2]= 0.00000000e+00, rbcA[3]= 6.35960000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.58990000e-01, rbcB[1]=-4.76980000e-01, rbcB[2]= 0.00000000e+00, rbcB[3]= 6.35960000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[150]=RBDIHS, rbcA[0]= 1.03637600e+01, rbcA[1]=-6.60654000e+00, rbcA[2]=-1.04934700e+01, rbcA[3]= 6.73624000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.03637600e+01, rbcB[1]=-6.60654000e+00, rbcB[2]=-1.04934700e+01, rbcB[3]= 6.73624000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[151]=RBDIHS, rbcA[0]= 5.00825000e+00, rbcA[1]=-1.69870000e+00, rbcA[2]=-3.72380000e-01, rbcA[3]=-2.93716000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.00825000e+00, rbcB[1]=-1.69870000e+00, rbcB[2]=-3.72380000e-01, rbcB[3]=-2.93716000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[152]=RBDIHS, rbcA[0]= 2.92880000e+00, rbcA[1]=-1.46440000e+00, rbcA[2]= 2.09200000e-01, rbcA[3]=-1.67360000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.92880000e+00, rbcB[1]=-1.46440000e+00, rbcB[2]= 2.09200000e-01, rbcB[3]=-1.67360000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[153]=RBDIHS, rbcA[0]= 5.77183000e+00, rbcA[1]=-2.67148000e+00, rbcA[2]= 9.58140000e-01, rbcA[3]=-4.05848000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.77183000e+00, rbcB[1]=-2.67148000e+00, rbcB[2]= 9.58140000e-01, rbcB[3]=-4.05848000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[154]=RBDIHS, rbcA[0]= 8.03330000e-01, rbcA[1]= 2.40999000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.21331000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.03330000e-01, rbcB[1]= 2.40999000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.21331000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[155]=RBDIHS, rbcA[0]= 2.05016000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.05016000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.05016000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.05016000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[156]=RBDIHS, rbcA[0]= 3.02879800e+01, rbcA[1]=-4.81160000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.02879800e+01, rbcB[1]=-4.81160000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[157]=RBDIHS, rbcA[0]= 2.54763800e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-2.54763800e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.54763800e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-2.54763800e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[158]=RBDIHS, rbcA[0]= 1.57025500e+01, rbcA[1]= 3.17565600e+01, rbcA[2]=-3.66936000e+00, rbcA[3]=-4.37897500e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.57025500e+01, rbcB[1]= 3.17565600e+01, rbcB[2]=-3.66936000e+00, rbcB[3]=-4.37897500e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[159]=RBDIHS, rbcA[0]=-1.03574900e+01, rbcA[1]=-2.95871600e+01, rbcA[2]=-1.16734000e+00, rbcA[3]= 4.11119900e+01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.03574900e+01, rbcB[1]=-2.95871600e+01, rbcB[2]=-1.16734000e+00, rbcB[3]= 4.11119900e+01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[160]=RBDIHS, rbcA[0]= 4.50199000e+00, rbcA[1]= 7.82410000e-01, rbcA[2]=-1.60247000e+00, rbcA[3]=-3.68192000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.50199000e+00, rbcB[1]= 7.82410000e-01, rbcB[2]=-1.60247000e+00, rbcB[3]=-3.68192000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[161]=RBDIHS, rbcA[0]= 4.22590000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]=-3.12964000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 4.22590000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]=-3.12964000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[162]=RBDIHS, rbcA[0]=-7.65670000e-01, rbcA[1]= 2.70705000e+00, rbcA[2]= 4.02501000e+00, rbcA[3]=-5.96639000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-7.65670000e-01, rbcB[1]= 2.70705000e+00, rbcB[2]= 4.02501000e+00, rbcB[3]=-5.96639000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[163]=RBDIHS, rbcA[0]= 9.66500000e-01, rbcA[1]= 2.89951000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.86601000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.66500000e-01, rbcB[1]= 2.89951000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.86601000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[164]=RBDIHS, rbcA[0]=-4.23421000e+00, rbcA[1]= 7.22159000e+00, rbcA[2]= 1.90790000e+00, rbcA[3]=-4.89528000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.23421000e+00, rbcB[1]= 7.22159000e+00, rbcB[2]= 1.90790000e+00, rbcB[3]=-4.89528000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[165]=RBDIHS, rbcA[0]= 3.03340000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.03340000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.03340000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.03340000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[166]=RBDIHS, rbcA[0]= 1.02319700e+01, rbcA[1]= 3.52083000e+00, rbcA[2]=-3.97899000e+00, rbcA[3]=-9.77382000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.02319700e+01, rbcB[1]= 3.52083000e+00, rbcB[2]=-3.97899000e+00, rbcB[3]=-9.77382000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[167]=RBDIHS, rbcA[0]= 5.49778000e+00, rbcA[1]= 1.41838000e+00, rbcA[2]=-6.91615000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 5.49778000e+00, rbcB[1]= 1.41838000e+00, rbcB[2]=-6.91615000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[168]=RBDIHS, rbcA[0]=-1.21755000e+00, rbcA[1]=-3.65264000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 4.87018000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.21755000e+00, rbcB[1]=-3.65264000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 4.87018000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[169]=RBDIHS, rbcA[0]=-1.26775000e+00, rbcA[1]= 3.02085000e+00, rbcA[2]= 1.74473000e+00, rbcA[3]=-3.49782000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.26775000e+00, rbcB[1]= 3.02085000e+00, rbcB[2]= 1.74473000e+00, rbcB[3]=-3.49782000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[170]=RBDIHS, rbcA[0]= 3.80117000e+00, rbcA[1]=-6.95172000e+00, rbcA[2]=-1.01671000e+00, rbcA[3]= 4.16726000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.80117000e+00, rbcB[1]=-6.95172000e+00, rbcB[2]=-1.01671000e+00, rbcB[3]= 4.16726000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[171]=RBDIHS, rbcA[0]= 3.70280000e-01, rbcA[1]= 1.11086000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-1.48114000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.70280000e-01, rbcB[1]= 1.11086000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-1.48114000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[172]=RBDIHS, rbcA[0]= 3.32042200e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.32042200e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.32042200e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.32042200e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[173]=RBDIHS, rbcA[0]= 1.63176000e+01, rbcA[1]= 0.00000000e+00, rbcA[2]=-1.63176000e+01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.63176000e+01, rbcB[1]= 0.00000000e+00, rbcB[2]=-1.63176000e+01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[174]=RBDIHS, rbcA[0]= 3.40787000e+00, rbcA[1]=-2.80537000e+00, rbcA[2]=-3.59820000e-01, rbcA[3]=-2.42670000e-01, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.40787000e+00, rbcB[1]=-2.80537000e+00, rbcB[2]=-3.59820000e-01, rbcB[3]=-2.42670000e-01, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[175]=RBDIHS, rbcA[0]=-1.62590200e+01, rbcA[1]= 9.08765000e+00, rbcA[2]= 7.17138000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.62590200e+01, rbcB[1]= 9.08765000e+00, rbcB[2]= 7.17138000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[176]=RBDIHS, rbcA[0]= 9.45590000e-01, rbcA[1]= 2.83675000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-3.78234000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 9.45590000e-01, rbcB[1]= 2.83675000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-3.78234000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[177]=RBDIHS, rbcA[0]=-1.50624000e+00, rbcA[1]= 5.37225000e+00, rbcA[2]= 1.17989000e+00, rbcA[3]=-5.04590000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-1.50624000e+00, rbcB[1]= 5.37225000e+00, rbcB[2]= 1.17989000e+00, rbcB[3]=-5.04590000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[178]=RBDIHS, rbcA[0]= 1.00416000e+00, rbcA[1]= 3.01248000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]=-4.01664000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 1.00416000e+00, rbcB[1]= 3.01248000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]=-4.01664000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[179]=RBDIHS, rbcA[0]= 8.79268000e+00, rbcA[1]=-1.18344400e+01, rbcA[2]= 1.07529000e+00, rbcA[3]= 1.96648000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 8.79268000e+00, rbcB[1]=-1.18344400e+01, rbcB[2]= 1.07529000e+00, rbcB[3]= 1.96648000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[180]=RBDIHS, rbcA[0]=-5.77392000e+00, rbcA[1]= 3.38485000e+00, rbcA[2]= 2.38906000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-5.77392000e+00, rbcB[1]= 3.38485000e+00, rbcB[2]= 2.38906000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[181]=RBDIHS, rbcA[0]=-9.08346000e+00, rbcA[1]= 9.75709000e+00, rbcA[2]= 3.45180000e+00, rbcA[3]=-4.12542000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-9.08346000e+00, rbcB[1]= 9.75709000e+00, rbcB[2]= 3.45180000e+00, rbcB[3]=-4.12542000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[182]=RBDIHS, rbcA[0]=-4.70700000e-01, rbcA[1]=-1.41210000e+00, rbcA[2]= 0.00000000e+00, rbcA[3]= 1.88280000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-4.70700000e-01, rbcB[1]=-1.41210000e+00, rbcB[2]= 0.00000000e+00, rbcB[3]= 1.88280000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[183]=RBDIHS, rbcA[0]= 3.43088000e+00, rbcA[1]= 0.00000000e+00, rbcA[2]=-3.43088000e+00, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 3.43088000e+00, rbcB[1]= 0.00000000e+00, rbcB[2]=-3.43088000e+00, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[184]=RBDIHS, rbcA[0]= 2.57316000e+00, rbcA[1]= 3.49782000e+00, rbcA[2]=-1.10039000e+00, rbcA[3]=-4.97059000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]= 2.57316000e+00, rbcB[1]= 3.49782000e+00, rbcB[2]=-1.10039000e+00, rbcB[3]=-4.97059000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[185]=RBDIHS, rbcA[0]=-8.22160000e-01, rbcA[1]= 1.12759000e+00, rbcA[2]=-3.05440000e-01, rbcA[3]= 0.00000000e+00, rbcA[4]= 0.00000000e+00, rbcA[5]= 0.00000000e+00
39: rbcB[0]=-8.22160000e-01, rbcB[1]= 1.12759000e+00, rbcB[2]=-3.05440000e-01, rbcB[3]= 0.00000000e+00, rbcB[4]= 0.00000000e+00, rbcB[5]= 0.00000000e+00
39: functype[186]=LJ14, c6A= 3.20536041e-04, c12A= 1.71928145e-07, c6B= 3.20536041e-04, c12B= 1.71928145e-07
39: functype[187]=LJ14, c6A= 1.30458481e-03, c12A= 1.92011187e-06, c6B= 1.30458481e-03, c12B= 1.92011187e-06
39: functype[188]=LJ14, c6A= 1.40760563e-03, c12A= 1.25315910e-06, c6B= 1.40760563e-03, c12B= 1.25315910e-06
39: functype[189]=LJ14, c6A= 1.67637339e-03, c12A= 1.97547221e-06, c6B= 1.67637339e-03, c12B= 1.97547221e-06
39: functype[190]=LJ14, c6A= 0.00000000e+00, c12A= 0.00000000e+00, c6B= 0.00000000e+00, c12B= 0.00000000e+00
39: functype[191]=LJ14, c6A= 2.49447081e-04, c12A= 1.67110056e-07, c6B= 2.49447081e-04, c12B= 1.67110056e-07
39: functype[192]=LJ14, c6A= 1.01525205e-03, c12A= 1.86630294e-06, c6B= 1.01525205e-03, c12B= 1.86630294e-06
39: functype[193]=LJ14, c6A= 6.12890625e-05, c12A= 1.49631500e-08, c6B= 6.12890625e-05, c12B= 1.49631500e-08
39: functype[194]=LJ14, c6A= 2.69145489e-04, c12A= 1.09064212e-07, c6B= 2.69145489e-04, c12B= 1.09064212e-07
39: functype[195]=LJ14, c6A= 1.09542476e-03, c12A= 1.21804075e-06, c6B= 1.09542476e-03, c12B= 1.21804075e-06
39: functype[196]=LJ14, c6A= 3.86982011e-04, c12A= 3.18863352e-07, c6B= 3.86982011e-04, c12B= 3.18863352e-07
39: functype[197]=LJ14, c6A= 1.57502055e-03, c12A= 3.56109993e-06, c6B= 1.57502055e-03, c12B= 3.56109993e-06
39: functype[198]=LJ14, c6A= 2.44342255e-03, c12A= 6.79494872e-06, c6B= 2.44342255e-03, c12B= 6.79494872e-06
39: functype[199]=LJ14, c6A= 1.40194280e-03, c12A= 2.15310613e-06, c6B= 1.40194280e-03, c12B= 2.15310613e-06
39: functype[200]=LJ14, c6A= 1.09101784e-03, c12A= 2.09276780e-06, c6B= 1.09101784e-03, c12B= 2.09276780e-06
39: functype[201]=LJ14, c6A= 2.68062710e-04, c12A= 1.87387876e-07, c6B= 2.68062710e-04, c12B= 1.87387876e-07
39: functype[202]=LJ14, c6A= 2.26258289e-04, c12A= 1.37484813e-07, c6B= 2.26258289e-04, c12B= 1.37484813e-07
39: functype[203]=LJ14, c6A= 2.43143395e-04, c12A= 1.54167785e-07, c6B= 2.43143395e-04, c12B= 1.54167785e-07
39: functype[204]=LJ14, c6A= 1.17243785e-03, c12A= 2.34671283e-06, c6B= 1.17243785e-03, c12B= 2.34671283e-06
39: functype[205]=LJ14, c6A= 1.69256051e-03, c12A= 3.99321842e-06, c6B= 1.69256051e-03, c12B= 3.99321842e-06
39: functype[206]=LJ14, c6A= 5.04237478e-05, c12A= 1.01280845e-08, c6B= 5.04237478e-05, c12B= 1.01280845e-08
39: functype[207]=LJ14, c6A= 2.34763367e-04, c12A= 1.14652101e-07, c6B= 2.34763367e-04, c12B= 1.14652101e-07
39: functype[208]=LJ14, c6A= 5.76812790e-05, c12A= 1.02660284e-08, c6B= 5.76812790e-05, c12B= 1.02660284e-08
39: functype[209]=LJ14, c6A= 3.60245183e-03, c12A= 5.76973368e-06, c6B= 3.60245183e-03, c12B= 5.76973368e-06
39: functype[210]=LJ14, c6A= 6.88817690e-04, c12A= 5.02148096e-07, c6B= 6.88817690e-04, c12B= 5.02148096e-07
39: functype[211]=LJ14, c6A= 4.34922716e-03, c12A= 1.07007298e-05, c6B= 4.34922716e-03, c12B= 1.07007298e-05
39: reppow = 12
39: fudgeQQ = 0.5
39: cmap
39: atomtypes:
39: atomtype[ 0]={atomnumber= 7}
39: atomtype[ 1]={atomnumber= 1}
39: atomtype[ 2]={atomnumber= 6}
39: atomtype[ 3]={atomnumber= 1}
39: atomtype[ 4]={atomnumber= 6}
39: atomtype[ 5]={atomnumber= 8}
39: atomtype[ 6]={atomnumber= 6}
39: atomtype[ 7]={atomnumber= 1}
39: atomtype[ 8]={atomnumber= 6}
39: atomtype[ 9]={atomnumber= 16}
39: moltype (0):
39: name="Protein_chain_B"
39: atoms:
39: atom (156):
39: atom[ 0]={type= 0, typeB= 0, ptype= Atom, m= 1.40027e+01, q=-3.00000e-01, mB= 1.40027e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 1]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 2]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 3]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 4]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 2.50000e-01, mB= 1.20110e+01, qB= 2.50000e-01, resind= 0, atomnumber= 6}
39: atom[ 5]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 6]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 7]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 8]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 9]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 10]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 11]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 12]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 0, atomnumber= 6}
39: atom[ 13]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 14]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 15]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 0, atomnumber= 6}
39: atom[ 16]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 17]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 0, atomnumber= 1}
39: atom[ 18]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-3.00000e-01, mB= 1.40067e+01, qB=-3.00000e-01, resind= 0, atomnumber= 7}
39: atom[ 19]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 20]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 21]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.30000e-01, mB= 1.00800e+00, qB= 3.30000e-01, resind= 0, atomnumber= 1}
39: atom[ 22]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 0, atomnumber= 6}
39: atom[ 23]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 0, atomnumber= 8}
39: atom[ 24]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 1, atomnumber= 7}
39: atom[ 25]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 1, atomnumber= 1}
39: atom[ 26]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 1, atomnumber= 6}
39: atom[ 27]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 28]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 1, atomnumber= 6}
39: atom[ 29]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 30]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 31]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 32]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 33]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 34]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 1, atomnumber= 6}
39: atom[ 35]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 36]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 37]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 1, atomnumber= 1}
39: atom[ 38]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 1, atomnumber= 6}
39: atom[ 39]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 1, atomnumber= 8}
39: atom[ 40]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 2, atomnumber= 7}
39: atom[ 41]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 2, atomnumber= 1}
39: atom[ 42]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 2, atomnumber= 6}
39: atom[ 43]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 44]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-03, mB= 1.20110e+01, qB=-5.00000e-03, resind= 2, atomnumber= 6}
39: atom[ 45]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 46]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 2, atomnumber= 1}
39: atom[ 47]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 48]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 49]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 50]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 51]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 52]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 53]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 54]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 55]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 56]={type= 6, typeB= 6, ptype= Atom, m= 1.20110e+01, q=-1.15000e-01, mB= 1.20110e+01, qB=-1.15000e-01, resind= 2, atomnumber= 6}
39: atom[ 57]={type= 7, typeB= 7, ptype= Atom, m= 1.00800e+00, q= 1.15000e-01, mB= 1.00800e+00, qB= 1.15000e-01, resind= 2, atomnumber= 1}
39: atom[ 58]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 2, atomnumber= 6}
39: atom[ 59]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 2, atomnumber= 8}
39: atom[ 60]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 3, atomnumber= 7}
39: atom[ 61]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 3, atomnumber= 1}
39: atom[ 62]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 8.00000e-02, mB= 1.20110e+01, qB= 8.00000e-02, resind= 3, atomnumber= 6}
39: atom[ 63]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 64]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 3, atomnumber= 1}
39: atom[ 65]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 3, atomnumber= 6}
39: atom[ 66]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 3, atomnumber= 8}
39: atom[ 67]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 68]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 4, atomnumber= 1}
39: atom[ 69]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 70]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 71]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 4, atomnumber= 6}
39: atom[ 72]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 73]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 74]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-5.00000e-02, mB= 1.20110e+01, qB=-5.00000e-02, resind= 4, atomnumber= 6}
39: atom[ 75]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 76]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 77]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.90000e-01, mB= 1.20110e+01, qB= 1.90000e-01, resind= 4, atomnumber= 6}
39: atom[ 78]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 79]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 4, atomnumber= 1}
39: atom[ 80]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-7.00000e-01, mB= 1.40067e+01, qB=-7.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 81]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.40000e-01, mB= 1.00800e+00, qB= 4.40000e-01, resind= 4, atomnumber= 1}
39: atom[ 82]={type= 8, typeB= 8, ptype= Atom, m= 1.20110e+01, q= 6.40000e-01, mB= 1.20110e+01, qB= 6.40000e-01, resind= 4, atomnumber= 6}
39: atom[ 83]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 84]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 85]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 86]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-8.00000e-01, mB= 1.40067e+01, qB=-8.00000e-01, resind= 4, atomnumber= 7}
39: atom[ 87]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 88]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 4.60000e-01, mB= 1.00800e+00, qB= 4.60000e-01, resind= 4, atomnumber= 1}
39: atom[ 89]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 4, atomnumber= 6}
39: atom[ 90]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 4, atomnumber= 8}
39: atom[ 91]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 5, atomnumber= 7}
39: atom[ 92]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 5, atomnumber= 1}
39: atom[ 93]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 5, atomnumber= 6}
39: atom[ 94]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 95]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 6.00000e-02, mB= 1.20110e+01, qB= 6.00000e-02, resind= 5, atomnumber= 6}
39: atom[ 96]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 97]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 5, atomnumber= 1}
39: atom[ 98]={type= 9, typeB= 9, ptype= Atom, m= 3.20600e+01, q=-3.35000e-01, mB= 3.20600e+01, qB=-3.35000e-01, resind= 5, atomnumber= 16}
39: atom[ 99]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 1.55000e-01, mB= 1.00800e+00, qB= 1.55000e-01, resind= 5, atomnumber= 1}
39: atom[ 100]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 5, atomnumber= 6}
39: atom[ 101]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 5, atomnumber= 8}
39: atom[ 102]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 6, atomnumber= 7}
39: atom[ 103]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 6, atomnumber= 1}
39: atom[ 104]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 6, atomnumber= 6}
39: atom[ 105]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 106]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 107]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 108]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 109]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-2.20000e-01, mB= 1.20110e+01, qB=-2.20000e-01, resind= 6, atomnumber= 6}
39: atom[ 110]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 111]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 6, atomnumber= 1}
39: atom[ 112]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 7.00000e-01, mB= 1.20110e+01, qB= 7.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 113]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 114]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-8.00000e-01, mB= 1.59994e+01, qB=-8.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 115]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 6, atomnumber= 6}
39: atom[ 116]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 6, atomnumber= 8}
39: atom[ 117]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 7, atomnumber= 7}
39: atom[ 118]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 7, atomnumber= 1}
39: atom[ 119]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 7, atomnumber= 6}
39: atom[ 120]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 121]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.20000e-01, mB= 1.20110e+01, qB=-1.20000e-01, resind= 7, atomnumber= 6}
39: atom[ 122]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 123]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 124]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-6.00000e-02, mB= 1.20110e+01, qB=-6.00000e-02, resind= 7, atomnumber= 6}
39: atom[ 125]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 126]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 127]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 128]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 129]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 130]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 7, atomnumber= 6}
39: atom[ 131]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 132]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 133]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 7, atomnumber= 1}
39: atom[ 134]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 7, atomnumber= 6}
39: atom[ 135]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 7, atomnumber= 8}
39: atom[ 136]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 8, atomnumber= 7}
39: atom[ 137]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 8, atomnumber= 1}
39: atom[ 138]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 8, atomnumber= 6}
39: atom[ 139]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 140]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 8, atomnumber= 6}
39: atom[ 141]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 142]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 143]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 8, atomnumber= 1}
39: atom[ 144]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 8, atomnumber= 6}
39: atom[ 145]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 8, atomnumber= 8}
39: atom[ 146]={type= 0, typeB= 0, ptype= Atom, m= 1.40067e+01, q=-5.00000e-01, mB= 1.40067e+01, qB=-5.00000e-01, resind= 9, atomnumber= 7}
39: atom[ 147]={type= 1, typeB= 1, ptype= Atom, m= 1.00800e+00, q= 3.00000e-01, mB= 1.00800e+00, qB= 3.00000e-01, resind= 9, atomnumber= 1}
39: atom[ 148]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q= 1.40000e-01, mB= 1.20110e+01, qB= 1.40000e-01, resind= 9, atomnumber= 6}
39: atom[ 149]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 150]={type= 2, typeB= 2, ptype= Atom, m= 1.20110e+01, q=-1.80000e-01, mB= 1.20110e+01, qB=-1.80000e-01, resind= 9, atomnumber= 6}
39: atom[ 151]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 152]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 153]={type= 3, typeB= 3, ptype= Atom, m= 1.00800e+00, q= 6.00000e-02, mB= 1.00800e+00, qB= 6.00000e-02, resind= 9, atomnumber= 1}
39: atom[ 154]={type= 4, typeB= 4, ptype= Atom, m= 1.20110e+01, q= 5.00000e-01, mB= 1.20110e+01, qB= 5.00000e-01, resind= 9, atomnumber= 6}
39: atom[ 155]={type= 5, typeB= 5, ptype= Atom, m= 1.59994e+01, q=-5.00000e-01, mB= 1.59994e+01, qB=-5.00000e-01, resind= 9, atomnumber= 8}
39: atom (156):
39: atom[0]={name="N"}
39: atom[1]={name="H1"}
39: atom[2]={name="H2"}
39: atom[3]={name="H3"}
39: atom[4]={name="CA"}
39: atom[5]={name="HA"}
39: atom[6]={name="CB"}
39: atom[7]={name="HB1"}
39: atom[8]={name="HB2"}
39: atom[9]={name="CG"}
39: atom[10]={name="HG1"}
39: atom[11]={name="HG2"}
39: atom[12]={name="CD"}
39: atom[13]={name="HD1"}
39: atom[14]={name="HD2"}
39: atom[15]={name="CE"}
39: atom[16]={name="HE1"}
39: atom[17]={name="HE2"}
39: atom[18]={name="NZ"}
39: atom[19]={name="HZ1"}
39: atom[20]={name="HZ2"}
39: atom[21]={name="HZ3"}
39: atom[22]={name="C"}
39: atom[23]={name="O"}
39: atom[24]={name="N"}
39: atom[25]={name="H"}
39: atom[26]={name="CA"}
39: atom[27]={name="HA"}
39: atom[28]={name="CB"}
39: atom[29]={name="HB"}
39: atom[30]={name="CG1"}
39: atom[31]={name="HG11"}
39: atom[32]={name="HG12"}
39: atom[33]={name="HG13"}
39: atom[34]={name="CG2"}
39: atom[35]={name="HG21"}
39: atom[36]={name="HG22"}
39: atom[37]={name="HG23"}
39: atom[38]={name="C"}
39: atom[39]={name="O"}
39: atom[40]={name="N"}
39: atom[41]={name="H"}
39: atom[42]={name="CA"}
39: atom[43]={name="HA"}
39: atom[44]={name="CB"}
39: atom[45]={name="HB1"}
39: atom[46]={name="HB2"}
39: atom[47]={name="CG"}
39: atom[48]={name="CD1"}
39: atom[49]={name="HD1"}
39: atom[50]={name="CD2"}
39: atom[51]={name="HD2"}
39: atom[52]={name="CE1"}
39: atom[53]={name="HE1"}
39: atom[54]={name="CE2"}
39: atom[55]={name="HE2"}
39: atom[56]={name="CZ"}
39: atom[57]={name="HZ"}
39: atom[58]={name="C"}
39: atom[59]={name="O"}
39: atom[60]={name="N"}
39: atom[61]={name="H"}
39: atom[62]={name="CA"}
39: atom[63]={name="HA1"}
39: atom[64]={name="HA2"}
39: atom[65]={name="C"}
39: atom[66]={name="O"}
39: atom[67]={name="N"}
39: atom[68]={name="H"}
39: atom[69]={name="CA"}
39: atom[70]={name="HA"}
39: atom[71]={name="CB"}
39: atom[72]={name="HB1"}
39: atom[73]={name="HB2"}
39: atom[74]={name="CG"}
39: atom[75]={name="HG1"}
39: atom[76]={name="HG2"}
39: atom[77]={name="CD"}
39: atom[78]={name="HD1"}
39: atom[79]={name="HD2"}
39: atom[80]={name="NE"}
39: atom[81]={name="HE"}
39: atom[82]={name="CZ"}
39: atom[83]={name="NH1"}
39: atom[84]={name="HH11"}
39: atom[85]={name="HH12"}
39: atom[86]={name="NH2"}
39: atom[87]={name="HH21"}
39: atom[88]={name="HH22"}
39: atom[89]={name="C"}
39: atom[90]={name="O"}
39: atom[91]={name="N"}
39: atom[92]={name="H"}
39: atom[93]={name="CA"}
39: atom[94]={name="HA"}
39: atom[95]={name="CB"}
39: atom[96]={name="HB1"}
39: atom[97]={name="HB2"}
39: atom[98]={name="SG"}
39: atom[99]={name="HG"}
39: atom[100]={name="C"}
39: atom[101]={name="O"}
39: atom[102]={name="N"}
39: atom[103]={name="H"}
39: atom[104]={name="CA"}
39: atom[105]={name="HA"}
39: atom[106]={name="CB"}
39: atom[107]={name="HB1"}
39: atom[108]={name="HB2"}
39: atom[109]={name="CG"}
39: atom[110]={name="HG1"}
39: atom[111]={name="HG2"}
39: atom[112]={name="CD"}
39: atom[113]={name="OE1"}
39: atom[114]={name="OE2"}
39: atom[115]={name="C"}
39: atom[116]={name="O"}
39: atom[117]={name="N"}
39: atom[118]={name="H"}
39: atom[119]={name="CA"}
39: atom[120]={name="HA"}
39: atom[121]={name="CB"}
39: atom[122]={name="HB1"}
39: atom[123]={name="HB2"}
39: atom[124]={name="CG"}
39: atom[125]={name="HG"}
39: atom[126]={name="CD1"}
39: atom[127]={name="HD11"}
39: atom[128]={name="HD12"}
39: atom[129]={name="HD13"}
39: atom[130]={name="CD2"}
39: atom[131]={name="HD21"}
39: atom[132]={name="HD22"}
39: atom[133]={name="HD23"}
39: atom[134]={name="C"}
39: atom[135]={name="O"}
39: atom[136]={name="N"}
39: atom[137]={name="H"}
39: atom[138]={name="CA"}
39: atom[139]={name="HA"}
39: atom[140]={name="CB"}
39: atom[141]={name="HB1"}
39: atom[142]={name="HB2"}
39: atom[143]={name="HB3"}
39: atom[144]={name="C"}
39: atom[145]={name="O"}
39: atom[146]={name="N"}
39: atom[147]={name="H"}
39: atom[148]={name="CA"}
39: atom[149]={name="HA"}
39: atom[150]={name="CB"}
39: atom[151]={name="HB1"}
39: atom[152]={name="HB2"}
39: atom[153]={name="HB3"}
39: atom[154]={name="C"}
39: atom[155]={name="O"}
39: type (156):
39: type[0]={name="opls_287",nameB="opls_287"}
39: type[1]={name="opls_290",nameB="opls_290"}
39: type[2]={name="opls_290",nameB="opls_290"}
39: type[3]={name="opls_290",nameB="opls_290"}
39: type[4]={name="opls_293B",nameB="opls_293B"}
39: type[5]={name="opls_140",nameB="opls_140"}
39: type[6]={name="opls_136",nameB="opls_136"}
39: type[7]={name="opls_140",nameB="opls_140"}
39: type[8]={name="opls_140",nameB="opls_140"}
39: type[9]={name="opls_136",nameB="opls_136"}
39: type[10]={name="opls_140",nameB="opls_140"}
39: type[11]={name="opls_140",nameB="opls_140"}
39: type[12]={name="opls_136",nameB="opls_136"}
39: type[13]={name="opls_140",nameB="opls_140"}
39: type[14]={name="opls_140",nameB="opls_140"}
39: type[15]={name="opls_292",nameB="opls_292"}
39: type[16]={name="opls_140",nameB="opls_140"}
39: type[17]={name="opls_140",nameB="opls_140"}
39: type[18]={name="opls_287",nameB="opls_287"}
39: type[19]={name="opls_290",nameB="opls_290"}
39: type[20]={name="opls_290",nameB="opls_290"}
39: type[21]={name="opls_290",nameB="opls_290"}
39: type[22]={name="opls_235",nameB="opls_235"}
39: type[23]={name="opls_236",nameB="opls_236"}
39: type[24]={name="opls_238",nameB="opls_238"}
39: type[25]={name="opls_241",nameB="opls_241"}
39: type[26]={name="opls_224B",nameB="opls_224B"}
39: type[27]={name="opls_140",nameB="opls_140"}
39: type[28]={name="opls_137",nameB="opls_137"}
39: type[29]={name="opls_140",nameB="opls_140"}
39: type[30]={name="opls_135",nameB="opls_135"}
39: type[31]={name="opls_140",nameB="opls_140"}
39: type[32]={name="opls_140",nameB="opls_140"}
39: type[33]={name="opls_140",nameB="opls_140"}
39: type[34]={name="opls_135",nameB="opls_135"}
39: type[35]={name="opls_140",nameB="opls_140"}
39: type[36]={name="opls_140",nameB="opls_140"}
39: type[37]={name="opls_140",nameB="opls_140"}
39: type[38]={name="opls_235",nameB="opls_235"}
39: type[39]={name="opls_236",nameB="opls_236"}
39: type[40]={name="opls_238",nameB="opls_238"}
39: type[41]={name="opls_241",nameB="opls_241"}
39: type[42]={name="opls_224B",nameB="opls_224B"}
39: type[43]={name="opls_140",nameB="opls_140"}
39: type[44]={name="opls_149",nameB="opls_149"}
39: type[45]={name="opls_140",nameB="opls_140"}
39: type[46]={name="opls_140",nameB="opls_140"}
39: type[47]={name="opls_145",nameB="opls_145"}
39: type[48]={name="opls_145",nameB="opls_145"}
39: type[49]={name="opls_146",nameB="opls_146"}
39: type[50]={name="opls_145",nameB="opls_145"}
39: type[51]={name="opls_146",nameB="opls_146"}
39: type[52]={name="opls_145",nameB="opls_145"}
39: type[53]={name="opls_146",nameB="opls_146"}
39: type[54]={name="opls_145",nameB="opls_145"}
39: type[55]={name="opls_146",nameB="opls_146"}
39: type[56]={name="opls_145",nameB="opls_145"}
39: type[57]={name="opls_146",nameB="opls_146"}
39: type[58]={name="opls_235",nameB="opls_235"}
39: type[59]={name="opls_236",nameB="opls_236"}
39: type[60]={name="opls_238",nameB="opls_238"}
39: type[61]={name="opls_241",nameB="opls_241"}
39: type[62]={name="opls_223B",nameB="opls_223B"}
39: type[63]={name="opls_140",nameB="opls_140"}
39: type[64]={name="opls_140",nameB="opls_140"}
39: type[65]={name="opls_235",nameB="opls_235"}
39: type[66]={name="opls_236",nameB="opls_236"}
39: type[67]={name="opls_238",nameB="opls_238"}
39: type[68]={name="opls_241",nameB="opls_241"}
39: type[69]={name="opls_224B",nameB="opls_224B"}
39: type[70]={name="opls_140",nameB="opls_140"}
39: type[71]={name="opls_136",nameB="opls_136"}
39: type[72]={name="opls_140",nameB="opls_140"}
39: type[73]={name="opls_140",nameB="opls_140"}
39: type[74]={name="opls_308",nameB="opls_308"}
39: type[75]={name="opls_140",nameB="opls_140"}
39: type[76]={name="opls_140",nameB="opls_140"}
39: type[77]={name="opls_307",nameB="opls_307"}
39: type[78]={name="opls_140",nameB="opls_140"}
39: type[79]={name="opls_140",nameB="opls_140"}
39: type[80]={name="opls_303",nameB="opls_303"}
39: type[81]={name="opls_304",nameB="opls_304"}
39: type[82]={name="opls_302",nameB="opls_302"}
39: type[83]={name="opls_300",nameB="opls_300"}
39: type[84]={name="opls_301",nameB="opls_301"}
39: type[85]={name="opls_301",nameB="opls_301"}
39: type[86]={name="opls_300",nameB="opls_300"}
39: type[87]={name="opls_301",nameB="opls_301"}
39: type[88]={name="opls_301",nameB="opls_301"}
39: type[89]={name="opls_235",nameB="opls_235"}
39: type[90]={name="opls_236",nameB="opls_236"}
39: type[91]={name="opls_238",nameB="opls_238"}
39: type[92]={name="opls_241",nameB="opls_241"}
39: type[93]={name="opls_224B",nameB="opls_224B"}
39: type[94]={name="opls_140",nameB="opls_140"}
39: type[95]={name="opls_206",nameB="opls_206"}
39: type[96]={name="opls_140",nameB="opls_140"}
39: type[97]={name="opls_140",nameB="opls_140"}
39: type[98]={name="opls_200",nameB="opls_200"}
39: type[99]={name="opls_204",nameB="opls_204"}
39: type[100]={name="opls_235",nameB="opls_235"}
39: type[101]={name="opls_236",nameB="opls_236"}
39: type[102]={name="opls_238",nameB="opls_238"}
39: type[103]={name="opls_241",nameB="opls_241"}
39: type[104]={name="opls_224B",nameB="opls_224B"}
39: type[105]={name="opls_140",nameB="opls_140"}
39: type[106]={name="opls_136",nameB="opls_136"}
39: type[107]={name="opls_140",nameB="opls_140"}
39: type[108]={name="opls_140",nameB="opls_140"}
39: type[109]={name="opls_274",nameB="opls_274"}
39: type[110]={name="opls_140",nameB="opls_140"}
39: type[111]={name="opls_140",nameB="opls_140"}
39: type[112]={name="opls_271",nameB="opls_271"}
39: type[113]={name="opls_272",nameB="opls_272"}
39: type[114]={name="opls_272",nameB="opls_272"}
39: type[115]={name="opls_235",nameB="opls_235"}
39: type[116]={name="opls_236",nameB="opls_236"}
39: type[117]={name="opls_238",nameB="opls_238"}
39: type[118]={name="opls_241",nameB="opls_241"}
39: type[119]={name="opls_224B",nameB="opls_224B"}
39: type[120]={name="opls_140",nameB="opls_140"}
39: type[121]={name="opls_136",nameB="opls_136"}
39: type[122]={name="opls_140",nameB="opls_140"}
39: type[123]={name="opls_140",nameB="opls_140"}
39: type[124]={name="opls_137",nameB="opls_137"}
39: type[125]={name="opls_140",nameB="opls_140"}
39: type[126]={name="opls_135",nameB="opls_135"}
39: type[127]={name="opls_140",nameB="opls_140"}
39: type[128]={name="opls_140",nameB="opls_140"}
39: type[129]={name="opls_140",nameB="opls_140"}
39: type[130]={name="opls_135",nameB="opls_135"}
39: type[131]={name="opls_140",nameB="opls_140"}
39: type[132]={name="opls_140",nameB="opls_140"}
39: type[133]={name="opls_140",nameB="opls_140"}
39: type[134]={name="opls_235",nameB="opls_235"}
39: type[135]={name="opls_236",nameB="opls_236"}
39: type[136]={name="opls_238",nameB="opls_238"}
39: type[137]={name="opls_241",nameB="opls_241"}
39: type[138]={name="opls_224B",nameB="opls_224B"}
39: type[139]={name="opls_140",nameB="opls_140"}
39: type[140]={name="opls_135",nameB="opls_135"}
39: type[141]={name="opls_140",nameB="opls_140"}
39: type[142]={name="opls_140",nameB="opls_140"}
39: type[143]={name="opls_140",nameB="opls_140"}
39: type[144]={name="opls_235",nameB="opls_235"}
39: type[145]={name="opls_236",nameB="opls_236"}
39: type[146]={name="opls_238",nameB="opls_238"}
39: type[147]={name="opls_241",nameB="opls_241"}
39: type[148]={name="opls_224B",nameB="opls_224B"}
39: type[149]={name="opls_140",nameB="opls_140"}
39: type[150]={name="opls_135",nameB="opls_135"}
39: type[151]={name="opls_140",nameB="opls_140"}
39: type[152]={name="opls_140",nameB="opls_140"}
39: type[153]={name="opls_140",nameB="opls_140"}
39: type[154]={name="opls_235",nameB="opls_235"}
39: type[155]={name="opls_236",nameB="opls_236"}
39: residue (10):
39: residue[0]={name="LYS", nr=1, ic=' '}
39: residue[1]={name="VAL", nr=2, ic=' '}
39: residue[2]={name="PHE", nr=3, ic=' '}
39: residue[3]={name="GLY", nr=4, ic=' '}
39: residue[4]={name="ARG", nr=5, ic=' '}
39: residue[5]={name="CYS", nr=6, ic=' '}
39: residue[6]={name="GLU", nr=7, ic=' '}
39: residue[7]={name="LEU", nr=8, ic=' '}
39: residue[8]={name="ALA", nr=9, ic=' '}
39: residue[9]={name="ALA", nr=10, ic=' '}
39: excls:
39: nr=156
39: nra=1828
39: excls[0][0..12]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[1][13..20]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[2][21..28]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[3][29..36]={0, 1, 2, 3, 4, 5, 6, 22}
39: excls[4][37..54]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22,
39: 23, 24, 25, 26}
39: excls[5][55..67]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24}
39: excls[6][68..86]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,
39: 14, 15, 22, 23, 24}
39: excls[7][87..97]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[8][98..108]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22}
39: excls[9][109..125]={0, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
39: 16, 17, 18, 22}
39: excls[10][126..136]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[11][137..147]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15}
39: excls[12][148..164]={4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16,
39: 17, 18, 19, 20, 21}
39: excls[13][165..175]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[14][176..186]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18}
39: excls[15][187..200]={6, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18,
39: 19, 20, 21}
39: excls[16][201..211]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[17][212..222]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[18][223..233]={9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21}
39: excls[19][234..241]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[20][242..249]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[21][250..257]={12, 15, 16, 17, 18, 19, 20, 21}
39: excls[22][258..275]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23, 24,
39: 25, 26, 27, 28, 38}
39: excls[23][276..284]={0, 4, 5, 6, 22, 23, 24, 25, 26}
39: excls[24][285..301]={0, 4, 5, 6, 22, 23, 24, 25, 26, 27, 28, 29,
39: 30, 34, 38, 39, 40}
39: excls[25][302..310]={4, 22, 23, 24, 25, 26, 27, 28, 38}
39: excls[26][311..332]={4, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31,
39: 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42}
39: excls[27][333..344]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40}
39: excls[28][345..362]={22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,
39: 34, 35, 36, 37, 38, 39, 40}
39: excls[29][363..376]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[30][377..390]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[31][391..398]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[32][399..406]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[33][407..414]={26, 28, 29, 30, 31, 32, 33, 34}
39: excls[34][415..428]={24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35,
39: 36, 37, 38}
39: excls[35][429..436]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[36][437..444]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[37][445..452]={26, 28, 29, 30, 34, 35, 36, 37}
39: excls[38][453..469]={22, 24, 25, 26, 27, 28, 29, 30, 34, 38, 39,
39: 40, 41, 42, 43, 44, 58}
39: excls[39][470..478]={24, 26, 27, 28, 38, 39, 40, 41, 42}
39: excls[40][479..495]={24, 26, 27, 28, 38, 39, 40, 41, 42, 43, 44,
39: 45, 46, 47, 58, 59, 60}
39: excls[41][496..504]={26, 38, 39, 40, 41, 42, 43, 44, 58}
39: excls[42][505..522]={26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47,
39: 48, 50, 58, 59, 60, 61, 62}
39: excls[43][523..534]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60}
39: excls[44][535..552]={38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49,
39: 50, 51, 52, 54, 58, 59, 60}
39: excls[45][553..562]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[46][563..572]={40, 42, 43, 44, 45, 46, 47, 48, 50, 58}
39: excls[47][573..589]={40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
39: 52, 53, 54, 55, 56, 58}
39: excls[48][590..603]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53,
39: 54, 56, 57}
39: excls[49][604..611]={44, 47, 48, 49, 50, 52, 53, 56}
39: excls[50][612..625]={42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54,
39: 55, 56, 57}
39: excls[51][626..633]={44, 47, 48, 50, 51, 54, 55, 56}
39: excls[52][634..644]={44, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57}
39: excls[53][645..652]={47, 48, 49, 52, 53, 54, 56, 57}
39: excls[54][653..663]={44, 47, 48, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[55][664..671]={47, 50, 51, 52, 54, 55, 56, 57}
39: excls[56][672..682]={47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57}
39: excls[57][683..690]={48, 50, 52, 53, 54, 55, 56, 57}
39: excls[58][691..707]={38, 40, 41, 42, 43, 44, 45, 46, 47, 58, 59,
39: 60, 61, 62, 63, 64, 65}
39: excls[59][708..716]={40, 42, 43, 44, 58, 59, 60, 61, 62}
39: excls[60][717..730]={40, 42, 43, 44, 58, 59, 60, 61, 62, 63, 64,
39: 65, 66, 67}
39: excls[61][731..739]={42, 58, 59, 60, 61, 62, 63, 64, 65}
39: excls[62][740..752]={42, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67,
39: 68, 69}
39: excls[63][753..761]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[64][762..770]={58, 60, 61, 62, 63, 64, 65, 66, 67}
39: excls[65][771..784]={58, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69,
39: 70, 71, 89}
39: excls[66][785..793]={60, 62, 63, 64, 65, 66, 67, 68, 69}
39: excls[67][794..810]={60, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71,
39: 72, 73, 74, 89, 90, 91}
39: excls[68][811..819]={62, 65, 66, 67, 68, 69, 70, 71, 89}
39: excls[69][820..838]={62, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74,
39: 75, 76, 77, 89, 90, 91, 92, 93}
39: excls[70][839..850]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89, 90,
39: 91}
39: excls[71][851..868]={65, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76,
39: 77, 78, 79, 80, 89, 90, 91}
39: excls[72][869..879]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[73][880..890]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 89}
39: excls[74][891..906]={67, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
39: 79, 80, 81, 82, 89}
39: excls[75][907..917]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[76][918..928]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80}
39: excls[77][929..943]={69, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
39: 81, 82, 83, 86}
39: excls[78][944..953]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[79][954..963]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82}
39: excls[80][964..979]={71, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83,
39: 84, 85, 86, 87, 88}
39: excls[81][980..988]={74, 77, 78, 79, 80, 81, 82, 83, 86}
39: excls[82][989..1001]={74, 77, 78, 79, 80, 81, 82, 83, 84, 85,
39: 86, 87, 88}
39: excls[83][1002..1011]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[84][1012..1017]={80, 82, 83, 84, 85, 86}
39: excls[85][1018..1023]={80, 82, 83, 84, 85, 86}
39: excls[86][1024..1033]={77, 80, 81, 82, 83, 84, 85, 86, 87, 88}
39: excls[87][1034..1039]={80, 82, 83, 86, 87, 88}
39: excls[88][1040..1045]={80, 82, 83, 86, 87, 88}
39: excls[89][1046..1062]={65, 67, 68, 69, 70, 71, 72, 73, 74, 89,
39: 90, 91, 92, 93, 94, 95, 100}
39: excls[90][1063..1071]={67, 69, 70, 71, 89, 90, 91, 92, 93}
39: excls[91][1072..1088]={67, 69, 70, 71, 89, 90, 91, 92, 93, 94,
39: 95, 96, 97, 98, 100, 101, 102}
39: excls[92][1089..1097]={69, 89, 90, 91, 92, 93, 94, 95, 100}
39: excls[93][1098..1114]={69, 89, 90, 91, 92, 93, 94, 95, 96, 97,
39: 98, 99, 100, 101, 102, 103, 104}
39: excls[94][1115..1126]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102}
39: excls[95][1127..1139]={89, 91, 92, 93, 94, 95, 96, 97, 98, 99,
39: 100, 101, 102}
39: excls[96][1140..1148]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[97][1149..1157]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[98][1158..1166]={91, 93, 94, 95, 96, 97, 98, 99, 100}
39: excls[99][1167..1172]={93, 95, 96, 97, 98, 99}
39: excls[100][1173..1189]={89, 91, 92, 93, 94, 95, 96, 97, 98, 100,
39: 101, 102, 103, 104, 105, 106, 115}
39: excls[101][1190..1198]={91, 93, 94, 95, 100, 101, 102, 103, 104}
39: excls[102][1199..1215]={91, 93, 94, 95, 100, 101, 102, 103, 104,
39: 105, 106, 107, 108, 109, 115, 116, 117}
39: excls[103][1216..1224]={93, 100, 101, 102, 103, 104, 105, 106,
39: 115}
39: excls[104][1225..1243]={93, 100, 101, 102, 103, 104, 105, 106,
39: 107, 108, 109, 110, 111, 112, 115, 116, 117, 118, 119}
39: excls[105][1244..1255]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117}
39: excls[106][1256..1272]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 110, 111, 112, 113, 114, 115, 116, 117}
39: excls[107][1273..1283]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[108][1284..1294]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 115}
39: excls[109][1295..1307]={102, 104, 105, 106, 107, 108, 109, 110,
39: 111, 112, 113, 114, 115}
39: excls[110][1308..1317]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[111][1318..1327]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[112][1328..1337]={104, 106, 107, 108, 109, 110, 111, 112,
39: 113, 114}
39: excls[113][1338..1344]={106, 109, 110, 111, 112, 113, 114}
39: excls[114][1345..1351]={106, 109, 110, 111, 112, 113, 114}
39: excls[115][1352..1368]={100, 102, 103, 104, 105, 106, 107, 108,
39: 109, 115, 116, 117, 118, 119, 120, 121, 134}
39: excls[116][1369..1377]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119}
39: excls[117][1378..1394]={102, 104, 105, 106, 115, 116, 117, 118,
39: 119, 120, 121, 122, 123, 124, 134, 135, 136}
39: excls[118][1395..1403]={104, 115, 116, 117, 118, 119, 120, 121,
39: 134}
39: excls[119][1404..1422]={104, 115, 116, 117, 118, 119, 120, 121,
39: 122, 123, 124, 125, 126, 130, 134, 135, 136, 137, 138}
39: excls[120][1423..1434]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136}
39: excls[121][1435..1455]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135,
39: 136}
39: excls[122][1456..1466]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[123][1467..1477]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 130, 134}
39: excls[124][1478..1494]={117, 119, 120, 121, 122, 123, 124, 125,
39: 126, 127, 128, 129, 130, 131, 132, 133, 134}
39: excls[125][1495..1508]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[126][1509..1522]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[127][1523..1530]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[128][1531..1538]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[129][1539..1546]={121, 124, 125, 126, 127, 128, 129, 130}
39: excls[130][1547..1560]={119, 121, 122, 123, 124, 125, 126, 127,
39: 128, 129, 130, 131, 132, 133}
39: excls[131][1561..1568]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[132][1569..1576]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[133][1577..1584]={121, 124, 125, 126, 130, 131, 132, 133}
39: excls[134][1585..1601]={115, 117, 118, 119, 120, 121, 122, 123,
39: 124, 134, 135, 136, 137, 138, 139, 140, 144}
39: excls[135][1602..1610]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138}
39: excls[136][1611..1627]={117, 119, 120, 121, 134, 135, 136, 137,
39: 138, 139, 140, 141, 142, 143, 144, 145, 146}
39: excls[137][1628..1636]={119, 134, 135, 136, 137, 138, 139, 140,
39: 144}
39: excls[138][1637..1652]={119, 134, 135, 136, 137, 138, 139, 140,
39: 141, 142, 143, 144, 145, 146, 147, 148}
39: excls[139][1653..1664]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[140][1665..1676]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146}
39: excls[141][1677..1684]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[142][1685..1692]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[143][1693..1700]={136, 138, 139, 140, 141, 142, 143, 144}
39: excls[144][1701..1717]={134, 136, 137, 138, 139, 140, 141, 142,
39: 143, 144, 145, 146, 147, 148, 149, 150, 154}
39: excls[145][1718..1726]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148}
39: excls[146][1727..1742]={136, 138, 139, 140, 144, 145, 146, 147,
39: 148, 149, 150, 151, 152, 153, 154, 155}
39: excls[147][1743..1751]={138, 144, 145, 146, 147, 148, 149, 150,
39: 154}
39: excls[148][1752..1764]={138, 144, 145, 146, 147, 148, 149, 150,
39: 151, 152, 153, 154, 155}
39: excls[149][1765..1775]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[150][1776..1786]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[151][1787..1794]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[152][1795..1802]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[153][1803..1810]={146, 148, 149, 150, 151, 152, 153, 154}
39: excls[154][1811..1821]={144, 146, 147, 148, 149, 150, 151, 152,
39: 153, 154, 155}
39: excls[155][1822..1827]={146, 148, 149, 150, 154, 155}
39: Bond:
39: nr: 468
39: iatoms:
39: 0 type=100 (BONDS) 0 1
39: 1 type=100 (BONDS) 0 2
39: 2 type=100 (BONDS) 0 3
39: 3 type=101 (BONDS) 0 4
39: 4 type=102 (BONDS) 4 5
39: 5 type=103 (BONDS) 4 6
39: 6 type=104 (BONDS) 4 22
39: 7 type=102 (BONDS) 6 7
39: 8 type=102 (BONDS) 6 8
39: 9 type=103 (BONDS) 6 9
39: 10 type=102 (BONDS) 9 10
39: 11 type=102 (BONDS) 9 11
39: 12 type=103 (BONDS) 9 12
39: 13 type=102 (BONDS) 12 13
39: 14 type=102 (BONDS) 12 14
39: 15 type=103 (BONDS) 12 15
39: 16 type=102 (BONDS) 15 16
39: 17 type=102 (BONDS) 15 17
39: 18 type=101 (BONDS) 15 18
39: 19 type=100 (BONDS) 18 19
39: 20 type=100 (BONDS) 18 20
39: 21 type=100 (BONDS) 18 21
39: 22 type=105 (BONDS) 22 23
39: 23 type=106 (BONDS) 22 24
39: 24 type=100 (BONDS) 24 25
39: 25 type=107 (BONDS) 24 26
39: 26 type=102 (BONDS) 26 27
39: 27 type=103 (BONDS) 26 28
39: 28 type=104 (BONDS) 26 38
39: 29 type=102 (BONDS) 28 29
39: 30 type=103 (BONDS) 28 30
39: 31 type=103 (BONDS) 28 34
39: 32 type=102 (BONDS) 30 31
39: 33 type=102 (BONDS) 30 32
39: 34 type=102 (BONDS) 30 33
39: 35 type=102 (BONDS) 34 35
39: 36 type=102 (BONDS) 34 36
39: 37 type=102 (BONDS) 34 37
39: 38 type=105 (BONDS) 38 39
39: 39 type=106 (BONDS) 38 40
39: 40 type=100 (BONDS) 40 41
39: 41 type=107 (BONDS) 40 42
39: 42 type=102 (BONDS) 42 43
39: 43 type=103 (BONDS) 42 44
39: 44 type=104 (BONDS) 42 58
39: 45 type=102 (BONDS) 44 45
39: 46 type=102 (BONDS) 44 46
39: 47 type=108 (BONDS) 44 47
39: 48 type=109 (BONDS) 47 48
39: 49 type=109 (BONDS) 47 50
39: 50 type=110 (BONDS) 48 49
39: 51 type=109 (BONDS) 48 52
39: 52 type=110 (BONDS) 50 51
39: 53 type=109 (BONDS) 50 54
39: 54 type=110 (BONDS) 52 53
39: 55 type=109 (BONDS) 52 56
39: 56 type=110 (BONDS) 54 55
39: 57 type=109 (BONDS) 54 56
39: 58 type=110 (BONDS) 56 57
39: 59 type=105 (BONDS) 58 59
39: 60 type=106 (BONDS) 58 60
39: 61 type=100 (BONDS) 60 61
39: 62 type=107 (BONDS) 60 62
39: 63 type=102 (BONDS) 62 63
39: 64 type=102 (BONDS) 62 64
39: 65 type=104 (BONDS) 62 65
39: 66 type=105 (BONDS) 65 66
39: 67 type=106 (BONDS) 65 67
39: 68 type=100 (BONDS) 67 68
39: 69 type=107 (BONDS) 67 69
39: 70 type=102 (BONDS) 69 70
39: 71 type=103 (BONDS) 69 71
39: 72 type=104 (BONDS) 69 89
39: 73 type=102 (BONDS) 71 72
39: 74 type=102 (BONDS) 71 73
39: 75 type=103 (BONDS) 71 74
39: 76 type=102 (BONDS) 74 75
39: 77 type=102 (BONDS) 74 76
39: 78 type=103 (BONDS) 74 77
39: 79 type=102 (BONDS) 77 78
39: 80 type=102 (BONDS) 77 79
39: 81 type=111 (BONDS) 77 80
39: 82 type=100 (BONDS) 80 81
39: 83 type=112 (BONDS) 80 82
39: 84 type=112 (BONDS) 82 83
39: 85 type=112 (BONDS) 82 86
39: 86 type=100 (BONDS) 83 84
39: 87 type=100 (BONDS) 83 85
39: 88 type=100 (BONDS) 86 87
39: 89 type=100 (BONDS) 86 88
39: 90 type=105 (BONDS) 89 90
39: 91 type=106 (BONDS) 89 91
39: 92 type=100 (BONDS) 91 92
39: 93 type=107 (BONDS) 91 93
39: 94 type=102 (BONDS) 93 94
39: 95 type=103 (BONDS) 93 95
39: 96 type=104 (BONDS) 93 100
39: 97 type=102 (BONDS) 95 96
39: 98 type=102 (BONDS) 95 97
39: 99 type=113 (BONDS) 95 98
39: 100 type=114 (BONDS) 98 99
39: 101 type=105 (BONDS) 100 101
39: 102 type=106 (BONDS) 100 102
39: 103 type=100 (BONDS) 102 103
39: 104 type=107 (BONDS) 102 104
39: 105 type=102 (BONDS) 104 105
39: 106 type=103 (BONDS) 104 106
39: 107 type=104 (BONDS) 104 115
39: 108 type=102 (BONDS) 106 107
39: 109 type=102 (BONDS) 106 108
39: 110 type=103 (BONDS) 106 109
39: 111 type=102 (BONDS) 109 110
39: 112 type=102 (BONDS) 109 111
39: 113 type=104 (BONDS) 109 112
39: 114 type=115 (BONDS) 112 113
39: 115 type=115 (BONDS) 112 114
39: 116 type=105 (BONDS) 115 116
39: 117 type=106 (BONDS) 115 117
39: 118 type=100 (BONDS) 117 118
39: 119 type=107 (BONDS) 117 119
39: 120 type=102 (BONDS) 119 120
39: 121 type=103 (BONDS) 119 121
39: 122 type=104 (BONDS) 119 134
39: 123 type=102 (BONDS) 121 122
39: 124 type=102 (BONDS) 121 123
39: 125 type=103 (BONDS) 121 124
39: 126 type=102 (BONDS) 124 125
39: 127 type=103 (BONDS) 124 126
39: 128 type=103 (BONDS) 124 130
39: 129 type=102 (BONDS) 126 127
39: 130 type=102 (BONDS) 126 128
39: 131 type=102 (BONDS) 126 129
39: 132 type=102 (BONDS) 130 131
39: 133 type=102 (BONDS) 130 132
39: 134 type=102 (BONDS) 130 133
39: 135 type=105 (BONDS) 134 135
39: 136 type=106 (BONDS) 134 136
39: 137 type=100 (BONDS) 136 137
39: 138 type=107 (BONDS) 136 138
39: 139 type=102 (BONDS) 138 139
39: 140 type=103 (BONDS) 138 140
39: 141 type=104 (BONDS) 138 144
39: 142 type=102 (BONDS) 140 141
39: 143 type=102 (BONDS) 140 142
39: 144 type=102 (BONDS) 140 143
39: 145 type=105 (BONDS) 144 145
39: 146 type=106 (BONDS) 144 146
39: 147 type=100 (BONDS) 146 147
39: 148 type=107 (BONDS) 146 148
39: 149 type=102 (BONDS) 148 149
39: 150 type=103 (BONDS) 148 150
39: 151 type=104 (BONDS) 148 154
39: 152 type=102 (BONDS) 150 151
39: 153 type=102 (BONDS) 150 152
39: 154 type=102 (BONDS) 150 153
39: 155 type=105 (BONDS) 154 155
39: G96Bond:
39: nr: 0
39: Morse:
39: nr: 0
39: Cubic Bonds:
39: nr: 0
39: Connect Bonds:
39: nr: 0
39: Harmonic Pot.:
39: nr: 0
39: FENE Bonds:
39: nr: 0
39: Tab. Bonds:
39: nr: 0
39: Tab. Bonds NC:
39: nr: 0
39: Restraint Pot.:
39: nr: 0
39: Angle:
39: nr: 1124
39: iatoms:
39: 0 type=116 (ANGLES) 1 0 2
39: 1 type=116 (ANGLES) 1 0 3
39: 2 type=116 (ANGLES) 1 0 4
39: 3 type=116 (ANGLES) 2 0 3
39: 4 type=116 (ANGLES) 2 0 4
39: 5 type=116 (ANGLES) 3 0 4
39: 6 type=116 (ANGLES) 0 4 5
39: 7 type=117 (ANGLES) 0 4 6
39: 8 type=117 (ANGLES) 0 4 22
39: 9 type=118 (ANGLES) 5 4 6
39: 10 type=116 (ANGLES) 5 4 22
39: 11 type=119 (ANGLES) 6 4 22
39: 12 type=118 (ANGLES) 4 6 7
39: 13 type=118 (ANGLES) 4 6 8
39: 14 type=120 (ANGLES) 4 6 9
39: 15 type=121 (ANGLES) 7 6 8
39: 16 type=118 (ANGLES) 7 6 9
39: 17 type=118 (ANGLES) 8 6 9
39: 18 type=118 (ANGLES) 6 9 10
39: 19 type=118 (ANGLES) 6 9 11
39: 20 type=120 (ANGLES) 6 9 12
39: 21 type=121 (ANGLES) 10 9 11
39: 22 type=118 (ANGLES) 10 9 12
39: 23 type=118 (ANGLES) 11 9 12
39: 24 type=118 (ANGLES) 9 12 13
39: 25 type=118 (ANGLES) 9 12 14
39: 26 type=120 (ANGLES) 9 12 15
39: 27 type=121 (ANGLES) 13 12 14
39: 28 type=118 (ANGLES) 13 12 15
39: 29 type=118 (ANGLES) 14 12 15
39: 30 type=118 (ANGLES) 12 15 16
39: 31 type=118 (ANGLES) 12 15 17
39: 32 type=117 (ANGLES) 12 15 18
39: 33 type=121 (ANGLES) 16 15 17
39: 34 type=116 (ANGLES) 16 15 18
39: 35 type=116 (ANGLES) 17 15 18
39: 36 type=116 (ANGLES) 15 18 19
39: 37 type=116 (ANGLES) 15 18 20
39: 38 type=116 (ANGLES) 15 18 21
39: 39 type=116 (ANGLES) 19 18 20
39: 40 type=116 (ANGLES) 19 18 21
39: 41 type=116 (ANGLES) 20 18 21
39: 42 type=122 (ANGLES) 4 22 23
39: 43 type=123 (ANGLES) 4 22 24
39: 44 type=124 (ANGLES) 23 22 24
39: 45 type=125 (ANGLES) 22 24 25
39: 46 type=126 (ANGLES) 22 24 26
39: 47 type=127 (ANGLES) 25 24 26
39: 48 type=116 (ANGLES) 24 26 27
39: 49 type=128 (ANGLES) 24 26 28
39: 50 type=129 (ANGLES) 24 26 38
39: 51 type=118 (ANGLES) 27 26 28
39: 52 type=116 (ANGLES) 27 26 38
39: 53 type=119 (ANGLES) 28 26 38
39: 54 type=118 (ANGLES) 26 28 29
39: 55 type=120 (ANGLES) 26 28 30
39: 56 type=120 (ANGLES) 26 28 34
39: 57 type=118 (ANGLES) 29 28 30
39: 58 type=118 (ANGLES) 29 28 34
39: 59 type=120 (ANGLES) 30 28 34
39: 60 type=118 (ANGLES) 28 30 31
39: 61 type=118 (ANGLES) 28 30 32
39: 62 type=118 (ANGLES) 28 30 33
39: 63 type=121 (ANGLES) 31 30 32
39: 64 type=121 (ANGLES) 31 30 33
39: 65 type=121 (ANGLES) 32 30 33
39: 66 type=118 (ANGLES) 28 34 35
39: 67 type=118 (ANGLES) 28 34 36
39: 68 type=118 (ANGLES) 28 34 37
39: 69 type=121 (ANGLES) 35 34 36
39: 70 type=121 (ANGLES) 35 34 37
39: 71 type=121 (ANGLES) 36 34 37
39: 72 type=122 (ANGLES) 26 38 39
39: 73 type=123 (ANGLES) 26 38 40
39: 74 type=124 (ANGLES) 39 38 40
39: 75 type=125 (ANGLES) 38 40 41
39: 76 type=126 (ANGLES) 38 40 42
39: 77 type=127 (ANGLES) 41 40 42
39: 78 type=116 (ANGLES) 40 42 43
39: 79 type=128 (ANGLES) 40 42 44
39: 80 type=129 (ANGLES) 40 42 58
39: 81 type=118 (ANGLES) 43 42 44
39: 82 type=116 (ANGLES) 43 42 58
39: 83 type=119 (ANGLES) 44 42 58
39: 84 type=118 (ANGLES) 42 44 45
39: 85 type=118 (ANGLES) 42 44 46
39: 86 type=130 (ANGLES) 42 44 47
39: 87 type=121 (ANGLES) 45 44 46
39: 88 type=116 (ANGLES) 45 44 47
39: 89 type=116 (ANGLES) 46 44 47
39: 90 type=131 (ANGLES) 44 47 48
39: 91 type=131 (ANGLES) 44 47 50
39: 92 type=132 (ANGLES) 48 47 50
39: 93 type=133 (ANGLES) 47 48 49
39: 94 type=132 (ANGLES) 47 48 52
39: 95 type=133 (ANGLES) 49 48 52
39: 96 type=133 (ANGLES) 47 50 51
39: 97 type=132 (ANGLES) 47 50 54
39: 98 type=133 (ANGLES) 51 50 54
39: 99 type=133 (ANGLES) 48 52 53
39: 100 type=132 (ANGLES) 48 52 56
39: 101 type=133 (ANGLES) 53 52 56
39: 102 type=133 (ANGLES) 50 54 55
39: 103 type=132 (ANGLES) 50 54 56
39: 104 type=133 (ANGLES) 55 54 56
39: 105 type=132 (ANGLES) 52 56 54
39: 106 type=133 (ANGLES) 52 56 57
39: 107 type=133 (ANGLES) 54 56 57
39: 108 type=122 (ANGLES) 42 58 59
39: 109 type=123 (ANGLES) 42 58 60
39: 110 type=124 (ANGLES) 59 58 60
39: 111 type=125 (ANGLES) 58 60 61
39: 112 type=126 (ANGLES) 58 60 62
39: 113 type=127 (ANGLES) 61 60 62
39: 114 type=116 (ANGLES) 60 62 63
39: 115 type=116 (ANGLES) 60 62 64
39: 116 type=129 (ANGLES) 60 62 65
39: 117 type=121 (ANGLES) 63 62 64
39: 118 type=116 (ANGLES) 63 62 65
39: 119 type=116 (ANGLES) 64 62 65
39: 120 type=122 (ANGLES) 62 65 66
39: 121 type=123 (ANGLES) 62 65 67
39: 122 type=124 (ANGLES) 66 65 67
39: 123 type=125 (ANGLES) 65 67 68
39: 124 type=126 (ANGLES) 65 67 69
39: 125 type=127 (ANGLES) 68 67 69
39: 126 type=116 (ANGLES) 67 69 70
39: 127 type=128 (ANGLES) 67 69 71
39: 128 type=129 (ANGLES) 67 69 89
39: 129 type=118 (ANGLES) 70 69 71
39: 130 type=116 (ANGLES) 70 69 89
39: 131 type=119 (ANGLES) 71 69 89
39: 132 type=118 (ANGLES) 69 71 72
39: 133 type=118 (ANGLES) 69 71 73
39: 134 type=120 (ANGLES) 69 71 74
39: 135 type=121 (ANGLES) 72 71 73
39: 136 type=118 (ANGLES) 72 71 74
39: 137 type=118 (ANGLES) 73 71 74
39: 138 type=118 (ANGLES) 71 74 75
39: 139 type=118 (ANGLES) 71 74 76
39: 140 type=120 (ANGLES) 71 74 77
39: 141 type=121 (ANGLES) 75 74 76
39: 142 type=118 (ANGLES) 75 74 77
39: 143 type=118 (ANGLES) 76 74 77
39: 144 type=118 (ANGLES) 74 77 78
39: 145 type=118 (ANGLES) 74 77 79
39: 146 type=117 (ANGLES) 74 77 80
39: 147 type=121 (ANGLES) 78 77 79
39: 148 type=116 (ANGLES) 78 77 80
39: 149 type=116 (ANGLES) 79 77 80
39: 150 type=134 (ANGLES) 77 80 81
39: 151 type=135 (ANGLES) 77 80 82
39: 152 type=133 (ANGLES) 81 80 82
39: 153 type=131 (ANGLES) 80 82 83
39: 154 type=131 (ANGLES) 80 82 86
39: 155 type=131 (ANGLES) 83 82 86
39: 156 type=133 (ANGLES) 82 83 84
39: 157 type=133 (ANGLES) 82 83 85
39: 158 type=133 (ANGLES) 84 83 85
39: 159 type=133 (ANGLES) 82 86 87
39: 160 type=133 (ANGLES) 82 86 88
39: 161 type=133 (ANGLES) 87 86 88
39: 162 type=122 (ANGLES) 69 89 90
39: 163 type=123 (ANGLES) 69 89 91
39: 164 type=124 (ANGLES) 90 89 91
39: 165 type=125 (ANGLES) 89 91 92
39: 166 type=126 (ANGLES) 89 91 93
39: 167 type=127 (ANGLES) 92 91 93
39: 168 type=116 (ANGLES) 91 93 94
39: 169 type=128 (ANGLES) 91 93 95
39: 170 type=129 (ANGLES) 91 93 100
39: 171 type=118 (ANGLES) 94 93 95
39: 172 type=116 (ANGLES) 94 93 100
39: 173 type=119 (ANGLES) 95 93 100
39: 174 type=118 (ANGLES) 93 95 96
39: 175 type=118 (ANGLES) 93 95 97
39: 176 type=136 (ANGLES) 93 95 98
39: 177 type=121 (ANGLES) 96 95 97
39: 178 type=116 (ANGLES) 96 95 98
39: 179 type=116 (ANGLES) 97 95 98
39: 180 type=137 (ANGLES) 95 98 99
39: 181 type=122 (ANGLES) 93 100 101
39: 182 type=123 (ANGLES) 93 100 102
39: 183 type=124 (ANGLES) 101 100 102
39: 184 type=125 (ANGLES) 100 102 103
39: 185 type=126 (ANGLES) 100 102 104
39: 186 type=127 (ANGLES) 103 102 104
39: 187 type=116 (ANGLES) 102 104 105
39: 188 type=128 (ANGLES) 102 104 106
39: 189 type=129 (ANGLES) 102 104 115
39: 190 type=118 (ANGLES) 105 104 106
39: 191 type=116 (ANGLES) 105 104 115
39: 192 type=119 (ANGLES) 106 104 115
39: 193 type=118 (ANGLES) 104 106 107
39: 194 type=118 (ANGLES) 104 106 108
39: 195 type=120 (ANGLES) 104 106 109
39: 196 type=121 (ANGLES) 107 106 108
39: 197 type=118 (ANGLES) 107 106 109
39: 198 type=118 (ANGLES) 108 106 109
39: 199 type=118 (ANGLES) 106 109 110
39: 200 type=118 (ANGLES) 106 109 111
39: 201 type=119 (ANGLES) 106 109 112
39: 202 type=121 (ANGLES) 110 109 111
39: 203 type=116 (ANGLES) 110 109 112
39: 204 type=116 (ANGLES) 111 109 112
39: 205 type=138 (ANGLES) 109 112 113
39: 206 type=138 (ANGLES) 109 112 114
39: 207 type=139 (ANGLES) 113 112 114
39: 208 type=122 (ANGLES) 104 115 116
39: 209 type=123 (ANGLES) 104 115 117
39: 210 type=124 (ANGLES) 116 115 117
39: 211 type=125 (ANGLES) 115 117 118
39: 212 type=126 (ANGLES) 115 117 119
39: 213 type=127 (ANGLES) 118 117 119
39: 214 type=116 (ANGLES) 117 119 120
39: 215 type=128 (ANGLES) 117 119 121
39: 216 type=129 (ANGLES) 117 119 134
39: 217 type=118 (ANGLES) 120 119 121
39: 218 type=116 (ANGLES) 120 119 134
39: 219 type=119 (ANGLES) 121 119 134
39: 220 type=118 (ANGLES) 119 121 122
39: 221 type=118 (ANGLES) 119 121 123
39: 222 type=120 (ANGLES) 119 121 124
39: 223 type=121 (ANGLES) 122 121 123
39: 224 type=118 (ANGLES) 122 121 124
39: 225 type=118 (ANGLES) 123 121 124
39: 226 type=118 (ANGLES) 121 124 125
39: 227 type=120 (ANGLES) 121 124 126
39: 228 type=120 (ANGLES) 121 124 130
39: 229 type=118 (ANGLES) 125 124 126
39: 230 type=118 (ANGLES) 125 124 130
39: 231 type=120 (ANGLES) 126 124 130
39: 232 type=118 (ANGLES) 124 126 127
39: 233 type=118 (ANGLES) 124 126 128
39: 234 type=118 (ANGLES) 124 126 129
39: 235 type=121 (ANGLES) 127 126 128
39: 236 type=121 (ANGLES) 127 126 129
39: 237 type=121 (ANGLES) 128 126 129
39: 238 type=118 (ANGLES) 124 130 131
39: 239 type=118 (ANGLES) 124 130 132
39: 240 type=118 (ANGLES) 124 130 133
39: 241 type=121 (ANGLES) 131 130 132
39: 242 type=121 (ANGLES) 131 130 133
39: 243 type=121 (ANGLES) 132 130 133
39: 244 type=122 (ANGLES) 119 134 135
39: 245 type=123 (ANGLES) 119 134 136
39: 246 type=124 (ANGLES) 135 134 136
39: 247 type=125 (ANGLES) 134 136 137
39: 248 type=126 (ANGLES) 134 136 138
39: 249 type=127 (ANGLES) 137 136 138
39: 250 type=116 (ANGLES) 136 138 139
39: 251 type=128 (ANGLES) 136 138 140
39: 252 type=129 (ANGLES) 136 138 144
39: 253 type=118 (ANGLES) 139 138 140
39: 254 type=116 (ANGLES) 139 138 144
39: 255 type=119 (ANGLES) 140 138 144
39: 256 type=118 (ANGLES) 138 140 141
39: 257 type=118 (ANGLES) 138 140 142
39: 258 type=118 (ANGLES) 138 140 143
39: 259 type=121 (ANGLES) 141 140 142
39: 260 type=121 (ANGLES) 141 140 143
39: 261 type=121 (ANGLES) 142 140 143
39: 262 type=122 (ANGLES) 138 144 145
39: 263 type=123 (ANGLES) 138 144 146
39: 264 type=124 (ANGLES) 145 144 146
39: 265 type=125 (ANGLES) 144 146 147
39: 266 type=126 (ANGLES) 144 146 148
39: 267 type=127 (ANGLES) 147 146 148
39: 268 type=116 (ANGLES) 146 148 149
39: 269 type=128 (ANGLES) 146 148 150
39: 270 type=129 (ANGLES) 146 148 154
39: 271 type=118 (ANGLES) 149 148 150
39: 272 type=116 (ANGLES) 149 148 154
39: 273 type=119 (ANGLES) 150 148 154
39: 274 type=118 (ANGLES) 148 150 151
39: 275 type=118 (ANGLES) 148 150 152
39: 276 type=118 (ANGLES) 148 150 153
39: 277 type=121 (ANGLES) 151 150 152
39: 278 type=121 (ANGLES) 151 150 153
39: 279 type=121 (ANGLES) 152 150 153
39: 280 type=122 (ANGLES) 148 154 155
39: G96Angle:
39: nr: 0
39: Restricted Angles:
39: nr: 0
39: Lin. Angle:
39: nr: 0
39: Bond-Cross:
39: nr: 0
39: BA-Cross:
39: nr: 0
39: U-B:
39: nr: 0
39: Quartic Angles:
39: nr: 0
39: Tab. Angles:
39: nr: 0
39: Proper Dih.:
39: nr: 145
39: iatoms:
39: 0 type=140 (PDIHS) 4 24 22 23
39: 1 type=141 (PDIHS) 22 26 24 25
39: 2 type=140 (PDIHS) 26 40 38 39
39: 3 type=141 (PDIHS) 38 42 40 41
39: 4 type=140 (PDIHS) 42 60 58 59
39: 5 type=142 (PDIHS) 44 47 50 48
39: 6 type=142 (PDIHS) 47 52 48 49
39: 7 type=142 (PDIHS) 47 54 50 51
39: 8 type=142 (PDIHS) 48 56 52 53
39: 9 type=142 (PDIHS) 50 56 54 55
39: 10 type=142 (PDIHS) 52 54 56 57
39: 11 type=141 (PDIHS) 58 62 60 61
39: 12 type=140 (PDIHS) 62 67 65 66
39: 13 type=141 (PDIHS) 65 69 67 68
39: 14 type=140 (PDIHS) 69 91 89 90
39: 15 type=141 (PDIHS) 77 82 80 81
39: 16 type=140 (PDIHS) 80 83 82 86
39: 17 type=141 (PDIHS) 82 84 83 85
39: 18 type=141 (PDIHS) 82 87 86 88
39: 19 type=141 (PDIHS) 89 93 91 92
39: 20 type=140 (PDIHS) 93 102 100 101
39: 21 type=141 (PDIHS) 100 104 102 103
39: 22 type=140 (PDIHS) 104 117 115 116
39: 23 type=140 (PDIHS) 109 113 112 114
39: 24 type=141 (PDIHS) 115 119 117 118
39: 25 type=140 (PDIHS) 119 136 134 135
39: 26 type=141 (PDIHS) 134 138 136 137
39: 27 type=140 (PDIHS) 138 146 144 145
39: 28 type=141 (PDIHS) 144 148 146 147
39: Ryckaert-Bell.:
39: nr: 1565
39: iatoms:
39: 0 type=143 (RBDIHS) 1 0 4 5
39: 1 type=144 (RBDIHS) 1 0 4 6
39: 2 type=144 (RBDIHS) 1 0 4 22
39: 3 type=143 (RBDIHS) 2 0 4 5
39: 4 type=144 (RBDIHS) 2 0 4 6
39: 5 type=144 (RBDIHS) 2 0 4 22
39: 6 type=143 (RBDIHS) 3 0 4 5
39: 7 type=144 (RBDIHS) 3 0 4 6
39: 8 type=144 (RBDIHS) 3 0 4 22
39: 9 type=145 (RBDIHS) 0 4 6 9
39: 10 type=146 (RBDIHS) 22 4 6 9
39: 11 type=147 (RBDIHS) 0 4 6 7
39: 12 type=147 (RBDIHS) 0 4 6 8
39: 13 type=148 (RBDIHS) 5 4 6 7
39: 14 type=148 (RBDIHS) 5 4 6 8
39: 15 type=148 (RBDIHS) 5 4 6 9
39: 16 type=149 (RBDIHS) 22 4 6 7
39: 17 type=149 (RBDIHS) 22 4 6 8
39: 18 type=150 (RBDIHS) 0 4 22 24
39: 19 type=151 (RBDIHS) 6 4 22 24
39: 20 type=148 (RBDIHS) 4 6 9 10
39: 21 type=148 (RBDIHS) 4 6 9 11
39: 22 type=152 (RBDIHS) 4 6 9 12
39: 23 type=148 (RBDIHS) 7 6 9 10
39: 24 type=148 (RBDIHS) 7 6 9 11
39: 25 type=148 (RBDIHS) 7 6 9 12
39: 26 type=148 (RBDIHS) 8 6 9 10
39: 27 type=148 (RBDIHS) 8 6 9 11
39: 28 type=148 (RBDIHS) 8 6 9 12
39: 29 type=148 (RBDIHS) 6 9 12 13
39: 30 type=148 (RBDIHS) 6 9 12 14
39: 31 type=152 (RBDIHS) 6 9 12 15
39: 32 type=148 (RBDIHS) 10 9 12 13
39: 33 type=148 (RBDIHS) 10 9 12 14
39: 34 type=148 (RBDIHS) 10 9 12 15
39: 35 type=148 (RBDIHS) 11 9 12 13
39: 36 type=148 (RBDIHS) 11 9 12 14
39: 37 type=148 (RBDIHS) 11 9 12 15
39: 38 type=148 (RBDIHS) 9 12 15 16
39: 39 type=148 (RBDIHS) 9 12 15 17
39: 40 type=153 (RBDIHS) 9 12 15 18
39: 41 type=148 (RBDIHS) 13 12 15 16
39: 42 type=148 (RBDIHS) 13 12 15 17
39: 43 type=154 (RBDIHS) 13 12 15 18
39: 44 type=148 (RBDIHS) 14 12 15 16
39: 45 type=148 (RBDIHS) 14 12 15 17
39: 46 type=154 (RBDIHS) 14 12 15 18
39: 47 type=144 (RBDIHS) 12 15 18 19
39: 48 type=144 (RBDIHS) 12 15 18 20
39: 49 type=144 (RBDIHS) 12 15 18 21
39: 50 type=143 (RBDIHS) 16 15 18 19
39: 51 type=143 (RBDIHS) 16 15 18 20
39: 52 type=143 (RBDIHS) 16 15 18 21
39: 53 type=143 (RBDIHS) 17 15 18 19
39: 54 type=143 (RBDIHS) 17 15 18 20
39: 55 type=143 (RBDIHS) 17 15 18 21
39: 56 type=155 (RBDIHS) 4 22 24 25
39: 57 type=156 (RBDIHS) 4 22 24 26
39: 58 type=155 (RBDIHS) 23 22 24 25
39: 59 type=157 (RBDIHS) 23 22 24 26
39: 60 type=158 (RBDIHS) 22 24 26 28
39: 61 type=159 (RBDIHS) 22 24 26 38
39: 62 type=160 (RBDIHS) 24 26 28 30
39: 63 type=160 (RBDIHS) 24 26 28 34
39: 64 type=161 (RBDIHS) 38 26 28 30
39: 65 type=161 (RBDIHS) 38 26 28 34
39: 66 type=147 (RBDIHS) 24 26 28 29
39: 67 type=148 (RBDIHS) 27 26 28 29
39: 68 type=148 (RBDIHS) 27 26 28 30
39: 69 type=148 (RBDIHS) 27 26 28 34
39: 70 type=149 (RBDIHS) 38 26 28 29
39: 71 type=150 (RBDIHS) 24 26 38 40
39: 72 type=151 (RBDIHS) 28 26 38 40
39: 73 type=148 (RBDIHS) 26 28 30 31
39: 74 type=148 (RBDIHS) 26 28 30 32
39: 75 type=148 (RBDIHS) 26 28 30 33
39: 76 type=148 (RBDIHS) 29 28 30 31
39: 77 type=148 (RBDIHS) 29 28 30 32
39: 78 type=148 (RBDIHS) 29 28 30 33
39: 79 type=148 (RBDIHS) 34 28 30 31
39: 80 type=148 (RBDIHS) 34 28 30 32
39: 81 type=148 (RBDIHS) 34 28 30 33
39: 82 type=148 (RBDIHS) 26 28 34 35
39: 83 type=148 (RBDIHS) 26 28 34 36
39: 84 type=148 (RBDIHS) 26 28 34 37
39: 85 type=148 (RBDIHS) 29 28 34 35
39: 86 type=148 (RBDIHS) 29 28 34 36
39: 87 type=148 (RBDIHS) 29 28 34 37
39: 88 type=148 (RBDIHS) 30 28 34 35
39: 89 type=148 (RBDIHS) 30 28 34 36
39: 90 type=148 (RBDIHS) 30 28 34 37
39: 91 type=155 (RBDIHS) 26 38 40 41
39: 92 type=156 (RBDIHS) 26 38 40 42
39: 93 type=155 (RBDIHS) 39 38 40 41
39: 94 type=157 (RBDIHS) 39 38 40 42
39: 95 type=158 (RBDIHS) 38 40 42 44
39: 96 type=159 (RBDIHS) 38 40 42 58
39: 97 type=147 (RBDIHS) 40 42 44 45
39: 98 type=147 (RBDIHS) 40 42 44 46
39: 99 type=162 (RBDIHS) 40 42 44 47
39: 100 type=148 (RBDIHS) 43 42 44 45
39: 101 type=148 (RBDIHS) 43 42 44 46
39: 102 type=163 (RBDIHS) 43 42 44 47
39: 103 type=149 (RBDIHS) 58 42 44 45
39: 104 type=149 (RBDIHS) 58 42 44 46
39: 105 type=164 (RBDIHS) 58 42 44 47
39: 106 type=150 (RBDIHS) 40 42 58 60
39: 107 type=151 (RBDIHS) 44 42 58 60
39: 108 type=165 (RBDIHS) 44 47 48 49
39: 109 type=165 (RBDIHS) 44 47 48 52
39: 110 type=165 (RBDIHS) 50 47 48 49
39: 111 type=165 (RBDIHS) 50 47 48 52
39: 112 type=165 (RBDIHS) 44 47 50 51
39: 113 type=165 (RBDIHS) 44 47 50 54
39: 114 type=165 (RBDIHS) 48 47 50 51
39: 115 type=165 (RBDIHS) 48 47 50 54
39: 116 type=165 (RBDIHS) 47 48 52 53
39: 117 type=165 (RBDIHS) 47 48 52 56
39: 118 type=165 (RBDIHS) 49 48 52 53
39: 119 type=165 (RBDIHS) 49 48 52 56
39: 120 type=165 (RBDIHS) 47 50 54 55
39: 121 type=165 (RBDIHS) 47 50 54 56
39: 122 type=165 (RBDIHS) 51 50 54 55
39: 123 type=165 (RBDIHS) 51 50 54 56
39: 124 type=165 (RBDIHS) 48 52 56 54
39: 125 type=165 (RBDIHS) 48 52 56 57
39: 126 type=165 (RBDIHS) 53 52 56 54
39: 127 type=165 (RBDIHS) 53 52 56 57
39: 128 type=165 (RBDIHS) 50 54 56 52
39: 129 type=165 (RBDIHS) 50 54 56 57
39: 130 type=165 (RBDIHS) 55 54 56 52
39: 131 type=165 (RBDIHS) 55 54 56 57
39: 132 type=155 (RBDIHS) 42 58 60 61
39: 133 type=156 (RBDIHS) 42 58 60 62
39: 134 type=155 (RBDIHS) 59 58 60 61
39: 135 type=157 (RBDIHS) 59 58 60 62
39: 136 type=159 (RBDIHS) 58 60 62 65
39: 137 type=150 (RBDIHS) 60 62 65 67
39: 138 type=155 (RBDIHS) 62 65 67 68
39: 139 type=156 (RBDIHS) 62 65 67 69
39: 140 type=155 (RBDIHS) 66 65 67 68
39: 141 type=157 (RBDIHS) 66 65 67 69
39: 142 type=158 (RBDIHS) 65 67 69 71
39: 143 type=159 (RBDIHS) 65 67 69 89
39: 144 type=166 (RBDIHS) 67 69 71 74
39: 145 type=167 (RBDIHS) 89 69 71 74
39: 146 type=147 (RBDIHS) 67 69 71 72
39: 147 type=147 (RBDIHS) 67 69 71 73
39: 148 type=148 (RBDIHS) 70 69 71 72
39: 149 type=148 (RBDIHS) 70 69 71 73
39: 150 type=148 (RBDIHS) 70 69 71 74
39: 151 type=149 (RBDIHS) 89 69 71 72
39: 152 type=149 (RBDIHS) 89 69 71 73
39: 153 type=150 (RBDIHS) 67 69 89 91
39: 154 type=151 (RBDIHS) 71 69 89 91
39: 155 type=148 (RBDIHS) 69 71 74 75
39: 156 type=148 (RBDIHS) 69 71 74 76
39: 157 type=152 (RBDIHS) 69 71 74 77
39: 158 type=148 (RBDIHS) 72 71 74 75
39: 159 type=148 (RBDIHS) 72 71 74 76
39: 160 type=148 (RBDIHS) 72 71 74 77
39: 161 type=148 (RBDIHS) 73 71 74 75
39: 162 type=148 (RBDIHS) 73 71 74 76
39: 163 type=148 (RBDIHS) 73 71 74 77
39: 164 type=148 (RBDIHS) 71 74 77 78
39: 165 type=148 (RBDIHS) 71 74 77 79
39: 166 type=153 (RBDIHS) 71 74 77 80
39: 167 type=148 (RBDIHS) 75 74 77 78
39: 168 type=148 (RBDIHS) 75 74 77 79
39: 169 type=168 (RBDIHS) 75 74 77 80
39: 170 type=148 (RBDIHS) 76 74 77 78
39: 171 type=148 (RBDIHS) 76 74 77 79
39: 172 type=168 (RBDIHS) 76 74 77 80
39: 173 type=169 (RBDIHS) 74 77 80 81
39: 174 type=170 (RBDIHS) 74 77 80 82
39: 175 type=171 (RBDIHS) 78 77 80 82
39: 176 type=171 (RBDIHS) 79 77 80 82
39: 177 type=172 (RBDIHS) 77 80 82 83
39: 178 type=172 (RBDIHS) 77 80 82 86
39: 179 type=173 (RBDIHS) 81 80 82 83
39: 180 type=173 (RBDIHS) 81 80 82 86
39: 181 type=173 (RBDIHS) 80 82 83 84
39: 182 type=173 (RBDIHS) 80 82 83 85
39: 183 type=173 (RBDIHS) 86 82 83 84
39: 184 type=173 (RBDIHS) 86 82 83 85
39: 185 type=173 (RBDIHS) 80 82 86 87
39: 186 type=173 (RBDIHS) 80 82 86 88
39: 187 type=173 (RBDIHS) 83 82 86 87
39: 188 type=173 (RBDIHS) 83 82 86 88
39: 189 type=155 (RBDIHS) 69 89 91 92
39: 190 type=156 (RBDIHS) 69 89 91 93
39: 191 type=155 (RBDIHS) 90 89 91 92
39: 192 type=157 (RBDIHS) 90 89 91 93
39: 193 type=158 (RBDIHS) 89 91 93 95
39: 194 type=159 (RBDIHS) 89 91 93 100
39: 195 type=174 (RBDIHS) 91 93 95 98
39: 196 type=175 (RBDIHS) 100 93 95 98
39: 197 type=147 (RBDIHS) 91 93 95 96
39: 198 type=147 (RBDIHS) 91 93 95 97
39: 199 type=148 (RBDIHS) 94 93 95 96
39: 200 type=148 (RBDIHS) 94 93 95 97
39: 201 type=176 (RBDIHS) 94 93 95 98
39: 202 type=149 (RBDIHS) 100 93 95 96
39: 203 type=149 (RBDIHS) 100 93 95 97
39: 204 type=150 (RBDIHS) 91 93 100 102
39: 205 type=151 (RBDIHS) 95 93 100 102
39: 206 type=177 (RBDIHS) 93 95 98 99
39: 207 type=178 (RBDIHS) 96 95 98 99
39: 208 type=178 (RBDIHS) 97 95 98 99
39: 209 type=155 (RBDIHS) 93 100 102 103
39: 210 type=156 (RBDIHS) 93 100 102 104
39: 211 type=155 (RBDIHS) 101 100 102 103
39: 212 type=157 (RBDIHS) 101 100 102 104
39: 213 type=158 (RBDIHS) 100 102 104 106
39: 214 type=159 (RBDIHS) 100 102 104 115
39: 215 type=179 (RBDIHS) 102 104 106 109
39: 216 type=180 (RBDIHS) 115 104 106 109
39: 217 type=147 (RBDIHS) 102 104 106 107
39: 218 type=147 (RBDIHS) 102 104 106 108
39: 219 type=148 (RBDIHS) 105 104 106 107
39: 220 type=148 (RBDIHS) 105 104 106 108
39: 221 type=148 (RBDIHS) 105 104 106 109
39: 222 type=149 (RBDIHS) 115 104 106 107
39: 223 type=149 (RBDIHS) 115 104 106 108
39: 224 type=150 (RBDIHS) 102 104 115 117
39: 225 type=151 (RBDIHS) 106 104 115 117
39: 226 type=148 (RBDIHS) 104 106 109 110
39: 227 type=148 (RBDIHS) 104 106 109 111
39: 228 type=181 (RBDIHS) 104 106 109 112
39: 229 type=148 (RBDIHS) 107 106 109 110
39: 230 type=148 (RBDIHS) 107 106 109 111
39: 231 type=182 (RBDIHS) 107 106 109 112
39: 232 type=148 (RBDIHS) 108 106 109 110
39: 233 type=148 (RBDIHS) 108 106 109 111
39: 234 type=182 (RBDIHS) 108 106 109 112
39: 235 type=183 (RBDIHS) 106 109 112 113
39: 236 type=183 (RBDIHS) 106 109 112 114
39: 237 type=155 (RBDIHS) 104 115 117 118
39: 238 type=156 (RBDIHS) 104 115 117 119
39: 239 type=155 (RBDIHS) 116 115 117 118
39: 240 type=157 (RBDIHS) 116 115 117 119
39: 241 type=158 (RBDIHS) 115 117 119 121
39: 242 type=159 (RBDIHS) 115 117 119 134
39: 243 type=184 (RBDIHS) 117 119 121 124
39: 244 type=185 (RBDIHS) 134 119 121 124
39: 245 type=147 (RBDIHS) 117 119 121 122
39: 246 type=147 (RBDIHS) 117 119 121 123
39: 247 type=148 (RBDIHS) 120 119 121 122
39: 248 type=148 (RBDIHS) 120 119 121 123
39: 249 type=148 (RBDIHS) 120 119 121 124
39: 250 type=149 (RBDIHS) 134 119 121 122
39: 251 type=149 (RBDIHS) 134 119 121 123
39: 252 type=150 (RBDIHS) 117 119 134 136
39: 253 type=151 (RBDIHS) 121 119 134 136
39: 254 type=148 (RBDIHS) 119 121 124 125
39: 255 type=152 (RBDIHS) 119 121 124 126
39: 256 type=152 (RBDIHS) 119 121 124 130
39: 257 type=148 (RBDIHS) 122 121 124 125
39: 258 type=148 (RBDIHS) 122 121 124 126
39: 259 type=148 (RBDIHS) 122 121 124 130
39: 260 type=148 (RBDIHS) 123 121 124 125
39: 261 type=148 (RBDIHS) 123 121 124 126
39: 262 type=148 (RBDIHS) 123 121 124 130
39: 263 type=148 (RBDIHS) 121 124 126 127
39: 264 type=148 (RBDIHS) 121 124 126 128
39: 265 type=148 (RBDIHS) 121 124 126 129
39: 266 type=148 (RBDIHS) 125 124 126 127
39: 267 type=148 (RBDIHS) 125 124 126 128
39: 268 type=148 (RBDIHS) 125 124 126 129
39: 269 type=148 (RBDIHS) 130 124 126 127
39: 270 type=148 (RBDIHS) 130 124 126 128
39: 271 type=148 (RBDIHS) 130 124 126 129
39: 272 type=148 (RBDIHS) 121 124 130 131
39: 273 type=148 (RBDIHS) 121 124 130 132
39: 274 type=148 (RBDIHS) 121 124 130 133
39: 275 type=148 (RBDIHS) 125 124 130 131
39: 276 type=148 (RBDIHS) 125 124 130 132
39: 277 type=148 (RBDIHS) 125 124 130 133
39: 278 type=148 (RBDIHS) 126 124 130 131
39: 279 type=148 (RBDIHS) 126 124 130 132
39: 280 type=148 (RBDIHS) 126 124 130 133
39: 281 type=155 (RBDIHS) 119 134 136 137
39: 282 type=156 (RBDIHS) 119 134 136 138
39: 283 type=155 (RBDIHS) 135 134 136 137
39: 284 type=157 (RBDIHS) 135 134 136 138
39: 285 type=158 (RBDIHS) 134 136 138 140
39: 286 type=159 (RBDIHS) 134 136 138 144
39: 287 type=147 (RBDIHS) 136 138 140 141
39: 288 type=147 (RBDIHS) 136 138 140 142
39: 289 type=147 (RBDIHS) 136 138 140 143
39: 290 type=148 (RBDIHS) 139 138 140 141
39: 291 type=148 (RBDIHS) 139 138 140 142
39: 292 type=148 (RBDIHS) 139 138 140 143
39: 293 type=149 (RBDIHS) 144 138 140 141
39: 294 type=149 (RBDIHS) 144 138 140 142
39: 295 type=149 (RBDIHS) 144 138 140 143
39: 296 type=150 (RBDIHS) 136 138 144 146
39: 297 type=151 (RBDIHS) 140 138 144 146
39: 298 type=155 (RBDIHS) 138 144 146 147
39: 299 type=156 (RBDIHS) 138 144 146 148
39: 300 type=155 (RBDIHS) 145 144 146 147
39: 301 type=157 (RBDIHS) 145 144 146 148
39: 302 type=158 (RBDIHS) 144 146 148 150
39: 303 type=159 (RBDIHS) 144 146 148 154
39: 304 type=147 (RBDIHS) 146 148 150 151
39: 305 type=147 (RBDIHS) 146 148 150 152
39: 306 type=147 (RBDIHS) 146 148 150 153
39: 307 type=148 (RBDIHS) 149 148 150 151
39: 308 type=148 (RBDIHS) 149 148 150 152
39: 309 type=148 (RBDIHS) 149 148 150 153
39: 310 type=149 (RBDIHS) 154 148 150 151
39: 311 type=149 (RBDIHS) 154 148 150 152
39: 312 type=149 (RBDIHS) 154 148 150 153
39: Restricted Dih.:
39: nr: 0
39: CBT Dih.:
39: nr: 0
39: Fourier Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Improper Dih.:
39: nr: 0
39: Tab. Dih.:
39: nr: 0
39: CMAP Dih.:
39: nr: 0
39: GB 1-2 Pol. (unused):
39: nr: 0
39: GB 1-3 Pol. (unused):
39: nr: 0
39: GB 1-4 Pol. (unused):
39: nr: 0
39: GB Polarization (unused):
39: nr: 0
39: Nonpolar Sol. (unused):
39: nr: 0
39: LJ-14:
39: nr: 1197
39: iatoms:
39: 0 type=186 (LJ14) 0 7
39: 1 type=186 (LJ14) 0 8
39: 2 type=187 (LJ14) 0 9
39: 3 type=188 (LJ14) 0 23
39: 4 type=189 (LJ14) 0 24
39: 5 type=190 (LJ14) 1 5
39: 6 type=190 (LJ14) 1 6
39: 7 type=190 (LJ14) 1 22
39: 8 type=190 (LJ14) 2 5
39: 9 type=190 (LJ14) 2 6
39: 10 type=190 (LJ14) 2 22
39: 11 type=190 (LJ14) 3 5
39: 12 type=190 (LJ14) 3 6
39: 13 type=190 (LJ14) 3 22
39: 14 type=191 (LJ14) 4 10
39: 15 type=191 (LJ14) 4 11
39: 16 type=192 (LJ14) 4 12
39: 17 type=190 (LJ14) 4 25
39: 18 type=192 (LJ14) 4 26
39: 19 type=193 (LJ14) 5 7
39: 20 type=193 (LJ14) 5 8
39: 21 type=191 (LJ14) 5 9
39: 22 type=194 (LJ14) 5 23
39: 23 type=186 (LJ14) 5 24
39: 24 type=191 (LJ14) 6 13
39: 25 type=191 (LJ14) 6 14
39: 26 type=192 (LJ14) 6 15
39: 27 type=195 (LJ14) 6 23
39: 28 type=187 (LJ14) 6 24
39: 29 type=193 (LJ14) 7 10
39: 30 type=193 (LJ14) 7 11
39: 31 type=191 (LJ14) 7 12
39: 32 type=196 (LJ14) 7 22
39: 33 type=193 (LJ14) 8 10
39: 34 type=193 (LJ14) 8 11
39: 35 type=191 (LJ14) 8 12
39: 36 type=196 (LJ14) 8 22
39: 37 type=191 (LJ14) 9 16
39: 38 type=191 (LJ14) 9 17
39: 39 type=187 (LJ14) 9 18
39: 40 type=197 (LJ14) 9 22
39: 41 type=193 (LJ14) 10 13
39: 42 type=193 (LJ14) 10 14
39: 43 type=191 (LJ14) 10 15
39: 44 type=193 (LJ14) 11 13
39: 45 type=193 (LJ14) 11 14
39: 46 type=191 (LJ14) 11 15
39: 47 type=190 (LJ14) 12 19
39: 48 type=190 (LJ14) 12 20
39: 49 type=190 (LJ14) 12 21
39: 50 type=193 (LJ14) 13 16
39: 51 type=193 (LJ14) 13 17
39: 52 type=186 (LJ14) 13 18
39: 53 type=193 (LJ14) 14 16
39: 54 type=193 (LJ14) 14 17
39: 55 type=186 (LJ14) 14 18
39: 56 type=190 (LJ14) 16 19
39: 57 type=190 (LJ14) 16 20
39: 58 type=190 (LJ14) 16 21
39: 59 type=190 (LJ14) 17 19
39: 60 type=190 (LJ14) 17 20
39: 61 type=190 (LJ14) 17 21
39: 62 type=196 (LJ14) 22 27
39: 63 type=197 (LJ14) 22 28
39: 64 type=198 (LJ14) 22 38
39: 65 type=190 (LJ14) 23 25
39: 66 type=195 (LJ14) 23 26
39: 67 type=186 (LJ14) 24 29
39: 68 type=187 (LJ14) 24 30
39: 69 type=187 (LJ14) 24 34
39: 70 type=188 (LJ14) 24 39
39: 71 type=189 (LJ14) 24 40
39: 72 type=190 (LJ14) 25 27
39: 73 type=190 (LJ14) 25 28
39: 74 type=190 (LJ14) 25 38
39: 75 type=191 (LJ14) 26 31
39: 76 type=191 (LJ14) 26 32
39: 77 type=191 (LJ14) 26 33
39: 78 type=191 (LJ14) 26 35
39: 79 type=191 (LJ14) 26 36
39: 80 type=191 (LJ14) 26 37
39: 81 type=190 (LJ14) 26 41
39: 82 type=192 (LJ14) 26 42
39: 83 type=193 (LJ14) 27 29
39: 84 type=191 (LJ14) 27 30
39: 85 type=191 (LJ14) 27 34
39: 86 type=194 (LJ14) 27 39
39: 87 type=186 (LJ14) 27 40
39: 88 type=195 (LJ14) 28 39
39: 89 type=187 (LJ14) 28 40
39: 90 type=193 (LJ14) 29 31
39: 91 type=193 (LJ14) 29 32
39: 92 type=193 (LJ14) 29 33
39: 93 type=193 (LJ14) 29 35
39: 94 type=193 (LJ14) 29 36
39: 95 type=193 (LJ14) 29 37
39: 96 type=196 (LJ14) 29 38
39: 97 type=191 (LJ14) 30 35
39: 98 type=191 (LJ14) 30 36
39: 99 type=191 (LJ14) 30 37
39: 100 type=197 (LJ14) 30 38
39: 101 type=191 (LJ14) 31 34
39: 102 type=191 (LJ14) 32 34
39: 103 type=191 (LJ14) 33 34
39: 104 type=197 (LJ14) 34 38
39: 105 type=196 (LJ14) 38 43
39: 106 type=197 (LJ14) 38 44
39: 107 type=198 (LJ14) 38 58
39: 108 type=190 (LJ14) 39 41
39: 109 type=195 (LJ14) 39 42
39: 110 type=186 (LJ14) 40 45
39: 111 type=186 (LJ14) 40 46
39: 112 type=199 (LJ14) 40 47
39: 113 type=188 (LJ14) 40 59
39: 114 type=189 (LJ14) 40 60
39: 115 type=190 (LJ14) 41 43
39: 116 type=190 (LJ14) 41 44
39: 117 type=190 (LJ14) 41 58
39: 118 type=200 (LJ14) 42 48
39: 119 type=200 (LJ14) 42 50
39: 120 type=190 (LJ14) 42 61
39: 121 type=192 (LJ14) 42 62
39: 122 type=193 (LJ14) 43 45
39: 123 type=193 (LJ14) 43 46
39: 124 type=201 (LJ14) 43 47
39: 125 type=194 (LJ14) 43 59
39: 126 type=186 (LJ14) 43 60
39: 127 type=202 (LJ14) 44 49
39: 128 type=202 (LJ14) 44 51
39: 129 type=200 (LJ14) 44 52
39: 130 type=200 (LJ14) 44 54
39: 131 type=195 (LJ14) 44 59
39: 132 type=187 (LJ14) 44 60
39: 133 type=201 (LJ14) 45 48
39: 134 type=201 (LJ14) 45 50
39: 135 type=196 (LJ14) 45 58
39: 136 type=201 (LJ14) 46 48
39: 137 type=201 (LJ14) 46 50
39: 138 type=196 (LJ14) 46 58
39: 139 type=203 (LJ14) 47 53
39: 140 type=203 (LJ14) 47 55
39: 141 type=204 (LJ14) 47 56
39: 142 type=205 (LJ14) 47 58
39: 143 type=203 (LJ14) 48 51
39: 144 type=204 (LJ14) 48 54
39: 145 type=203 (LJ14) 48 57
39: 146 type=203 (LJ14) 49 50
39: 147 type=206 (LJ14) 49 53
39: 148 type=203 (LJ14) 49 56
39: 149 type=204 (LJ14) 50 52
39: 150 type=203 (LJ14) 50 57
39: 151 type=206 (LJ14) 51 55
39: 152 type=203 (LJ14) 51 56
39: 153 type=203 (LJ14) 52 55
39: 154 type=203 (LJ14) 53 54
39: 155 type=206 (LJ14) 53 57
39: 156 type=206 (LJ14) 55 57
39: 157 type=196 (LJ14) 58 63
39: 158 type=196 (LJ14) 58 64
39: 159 type=198 (LJ14) 58 65
39: 160 type=190 (LJ14) 59 61
39: 161 type=195 (LJ14) 59 62
39: 162 type=188 (LJ14) 60 66
39: 163 type=189 (LJ14) 60 67
39: 164 type=190 (LJ14) 61 63
39: 165 type=190 (LJ14) 61 64
39: 166 type=190 (LJ14) 61 65
39: 167 type=190 (LJ14) 62 68
39: 168 type=192 (LJ14) 62 69
39: 169 type=194 (LJ14) 63 66
39: 170 type=186 (LJ14) 63 67
39: 171 type=194 (LJ14) 64 66
39: 172 type=186 (LJ14) 64 67
39: 173 type=196 (LJ14) 65 70
39: 174 type=197 (LJ14) 65 71
39: 175 type=198 (LJ14) 65 89
39: 176 type=190 (LJ14) 66 68
39: 177 type=195 (LJ14) 66 69
39: 178 type=186 (LJ14) 67 72
39: 179 type=186 (LJ14) 67 73
39: 180 type=187 (LJ14) 67 74
39: 181 type=188 (LJ14) 67 90
39: 182 type=189 (LJ14) 67 91
39: 183 type=190 (LJ14) 68 70
39: 184 type=190 (LJ14) 68 71
39: 185 type=190 (LJ14) 68 89
39: 186 type=191 (LJ14) 69 75
39: 187 type=191 (LJ14) 69 76
39: 188 type=192 (LJ14) 69 77
39: 189 type=190 (LJ14) 69 92
39: 190 type=192 (LJ14) 69 93
39: 191 type=193 (LJ14) 70 72
39: 192 type=193 (LJ14) 70 73
39: 193 type=191 (LJ14) 70 74
39: 194 type=194 (LJ14) 70 90
39: 195 type=186 (LJ14) 70 91
39: 196 type=191 (LJ14) 71 78
39: 197 type=191 (LJ14) 71 79
39: 198 type=187 (LJ14) 71 80
39: 199 type=195 (LJ14) 71 90
39: 200 type=187 (LJ14) 71 91
39: 201 type=193 (LJ14) 72 75
39: 202 type=193 (LJ14) 72 76
39: 203 type=191 (LJ14) 72 77
39: 204 type=196 (LJ14) 72 89
39: 205 type=193 (LJ14) 73 75
39: 206 type=193 (LJ14) 73 76
39: 207 type=191 (LJ14) 73 77
39: 208 type=196 (LJ14) 73 89
39: 209 type=190 (LJ14) 74 81
39: 210 type=207 (LJ14) 74 82
39: 211 type=197 (LJ14) 74 89
39: 212 type=193 (LJ14) 75 78
39: 213 type=193 (LJ14) 75 79
39: 214 type=186 (LJ14) 75 80
39: 215 type=193 (LJ14) 76 78
39: 216 type=193 (LJ14) 76 79
39: 217 type=186 (LJ14) 76 80
39: 218 type=187 (LJ14) 77 83
39: 219 type=187 (LJ14) 77 86
39: 220 type=190 (LJ14) 78 81
39: 221 type=208 (LJ14) 78 82
39: 222 type=190 (LJ14) 79 81
39: 223 type=208 (LJ14) 79 82
39: 224 type=190 (LJ14) 80 84
39: 225 type=190 (LJ14) 80 85
39: 226 type=190 (LJ14) 80 87
39: 227 type=190 (LJ14) 80 88
39: 228 type=190 (LJ14) 81 83
39: 229 type=190 (LJ14) 81 86
39: 230 type=190 (LJ14) 83 87
39: 231 type=190 (LJ14) 83 88
39: 232 type=190 (LJ14) 84 86
39: 233 type=190 (LJ14) 85 86
39: 234 type=196 (LJ14) 89 94
39: 235 type=197 (LJ14) 89 95
39: 236 type=198 (LJ14) 89 100
39: 237 type=190 (LJ14) 90 92
39: 238 type=195 (LJ14) 90 93
39: 239 type=186 (LJ14) 91 96
39: 240 type=186 (LJ14) 91 97
39: 241 type=209 (LJ14) 91 98
39: 242 type=188 (LJ14) 91 101
39: 243 type=189 (LJ14) 91 102
39: 244 type=190 (LJ14) 92 94
39: 245 type=190 (LJ14) 92 95
39: 246 type=190 (LJ14) 92 100
39: 247 type=190 (LJ14) 93 99
39: 248 type=190 (LJ14) 93 103
39: 249 type=192 (LJ14) 93 104
39: 250 type=193 (LJ14) 94 96
39: 251 type=193 (LJ14) 94 97
39: 252 type=210 (LJ14) 94 98
39: 253 type=194 (LJ14) 94 101
39: 254 type=186 (LJ14) 94 102
39: 255 type=195 (LJ14) 95 101
39: 256 type=187 (LJ14) 95 102
39: 257 type=190 (LJ14) 96 99
39: 258 type=196 (LJ14) 96 100
39: 259 type=190 (LJ14) 97 99
39: 260 type=196 (LJ14) 97 100
39: 261 type=211 (LJ14) 98 100
39: 262 type=196 (LJ14) 100 105
39: 263 type=197 (LJ14) 100 106
39: 264 type=198 (LJ14) 100 115
39: 265 type=190 (LJ14) 101 103
39: 266 type=195 (LJ14) 101 104
39: 267 type=186 (LJ14) 102 107
39: 268 type=186 (LJ14) 102 108
39: 269 type=187 (LJ14) 102 109
39: 270 type=188 (LJ14) 102 116
39: 271 type=189 (LJ14) 102 117
39: 272 type=190 (LJ14) 103 105
39: 273 type=190 (LJ14) 103 106
39: 274 type=190 (LJ14) 103 115
39: 275 type=191 (LJ14) 104 110
39: 276 type=191 (LJ14) 104 111
39: 277 type=197 (LJ14) 104 112
39: 278 type=190 (LJ14) 104 118
39: 279 type=192 (LJ14) 104 119
39: 280 type=193 (LJ14) 105 107
39: 281 type=193 (LJ14) 105 108
39: 282 type=191 (LJ14) 105 109
39: 283 type=194 (LJ14) 105 116
39: 284 type=186 (LJ14) 105 117
39: 285 type=195 (LJ14) 106 113
39: 286 type=195 (LJ14) 106 114
39: 287 type=195 (LJ14) 106 116
39: 288 type=187 (LJ14) 106 117
39: 289 type=193 (LJ14) 107 110
39: 290 type=193 (LJ14) 107 111
39: 291 type=196 (LJ14) 107 112
39: 292 type=196 (LJ14) 107 115
39: 293 type=193 (LJ14) 108 110
39: 294 type=193 (LJ14) 108 111
39: 295 type=196 (LJ14) 108 112
39: 296 type=196 (LJ14) 108 115
39: 297 type=197 (LJ14) 109 115
39: 298 type=194 (LJ14) 110 113
39: 299 type=194 (LJ14) 110 114
39: 300 type=194 (LJ14) 111 113
39: 301 type=194 (LJ14) 111 114
39: 302 type=196 (LJ14) 115 120
39: 303 type=197 (LJ14) 115 121
39: 304 type=198 (LJ14) 115 134
39: 305 type=190 (LJ14) 116 118
39: 306 type=195 (LJ14) 116 119
39: 307 type=186 (LJ14) 117 122
39: 308 type=186 (LJ14) 117 123
39: 309 type=187 (LJ14) 117 124
39: 310 type=188 (LJ14) 117 135
39: 311 type=189 (LJ14) 117 136
39: 312 type=190 (LJ14) 118 120
39: 313 type=190 (LJ14) 118 121
39: 314 type=190 (LJ14) 118 134
39: 315 type=191 (LJ14) 119 125
39: 316 type=192 (LJ14) 119 126
39: 317 type=192 (LJ14) 119 130
39: 318 type=190 (LJ14) 119 137
39: 319 type=192 (LJ14) 119 138
39: 320 type=193 (LJ14) 120 122
39: 321 type=193 (LJ14) 120 123
39: 322 type=191 (LJ14) 120 124
39: 323 type=194 (LJ14) 120 135
39: 324 type=186 (LJ14) 120 136
39: 325 type=191 (LJ14) 121 127
39: 326 type=191 (LJ14) 121 128
39: 327 type=191 (LJ14) 121 129
39: 328 type=191 (LJ14) 121 131
39: 329 type=191 (LJ14) 121 132
39: 330 type=191 (LJ14) 121 133
39: 331 type=195 (LJ14) 121 135
39: 332 type=187 (LJ14) 121 136
39: 333 type=193 (LJ14) 122 125
39: 334 type=191 (LJ14) 122 126
39: 335 type=191 (LJ14) 122 130
39: 336 type=196 (LJ14) 122 134
39: 337 type=193 (LJ14) 123 125
39: 338 type=191 (LJ14) 123 126
39: 339 type=191 (LJ14) 123 130
39: 340 type=196 (LJ14) 123 134
39: 341 type=197 (LJ14) 124 134
39: 342 type=193 (LJ14) 125 127
39: 343 type=193 (LJ14) 125 128
39: 344 type=193 (LJ14) 125 129
39: 345 type=193 (LJ14) 125 131
39: 346 type=193 (LJ14) 125 132
39: 347 type=193 (LJ14) 125 133
39: 348 type=191 (LJ14) 126 131
39: 349 type=191 (LJ14) 126 132
39: 350 type=191 (LJ14) 126 133
39: 351 type=191 (LJ14) 127 130
39: 352 type=191 (LJ14) 128 130
39: 353 type=191 (LJ14) 129 130
39: 354 type=196 (LJ14) 134 139
39: 355 type=197 (LJ14) 134 140
39: 356 type=198 (LJ14) 134 144
39: 357 type=190 (LJ14) 135 137
39: 358 type=195 (LJ14) 135 138
39: 359 type=186 (LJ14) 136 141
39: 360 type=186 (LJ14) 136 142
39: 361 type=186 (LJ14) 136 143
39: 362 type=188 (LJ14) 136 145
39: 363 type=189 (LJ14) 136 146
39: 364 type=190 (LJ14) 137 139
39: 365 type=190 (LJ14) 137 140
39: 366 type=190 (LJ14) 137 144
39: 367 type=190 (LJ14) 138 147
39: 368 type=192 (LJ14) 138 148
39: 369 type=193 (LJ14) 139 141
39: 370 type=193 (LJ14) 139 142
39: 371 type=193 (LJ14) 139 143
39: 372 type=194 (LJ14) 139 145
39: 373 type=186 (LJ14) 139 146
39: 374 type=195 (LJ14) 140 145
39: 375 type=187 (LJ14) 140 146
39: 376 type=196 (LJ14) 141 144
39: 377 type=196 (LJ14) 142 144
39: 378 type=196 (LJ14) 143 144
39: 379 type=196 (LJ14) 144 149
39: 380 type=197 (LJ14) 144 150
39: 381 type=198 (LJ14) 144 154
39: 382 type=190 (LJ14) 145 147
39: 383 type=195 (LJ14) 145 148
39: 384 type=186 (LJ14) 146 151
39: 385 type=186 (LJ14) 146 152
39: 386 type=186 (LJ14) 146 153
39: 387 type=188 (LJ14) 146 155
39: 388 type=190 (LJ14) 147 149
39: 389 type=190 (LJ14) 147 150
39: 390 type=190 (LJ14) 147 154
39: 391 type=193 (LJ14) 149 151
39: 392 type=193 (LJ14) 149 152
39: 393 type=193 (LJ14) 149 153
39: 394 type=194 (LJ14) 149 155
39: 395 type=195 (LJ14) 150 155
39: 396 type=196 (LJ14) 151 154
39: 397 type=196 (LJ14) 152 154
39: 398 type=196 (LJ14) 153 154
39: Coulomb-14:
39: nr: 0
39: LJC-14 q:
39: nr: 0
39: LJC Pairs NB:
39: nr: 0
39: LJ (SR):
39: nr: 0
39: Buck.ham (SR):
39: nr: 0
39: LJ (unused):
39: nr: 0
39: B.ham (unused):
39: nr: 0
39: Disper. corr.:
39: nr: 0
39: Coulomb (SR):
39: nr: 0
39: Coul (unused):
39: nr: 0
39: RF excl.:
39: nr: 0
39: Coul. recip.:
39: nr: 0
39: LJ recip.:
39: nr: 0
39: DPD:
39: nr: 0
39: Polarization:
39: nr: 0
39: Water Pol.:
39: nr: 0
39: Thole Pol.:
39: nr: 0
39: Anharm. Pol.:
39: nr: 0
39: Position Rest.:
39: nr: 0
39: Flat-bottom posres:
39: nr: 0
39: Dis. Rest.:
39: nr: 0
39: D.R.Viol. (nm):
39: nr: 0
39: Orient. Rest.:
39: nr: 0
39: Ori. R. RMSD:
39: nr: 0
39: Angle Rest.:
39: nr: 0
39: Angle Rest. Z:
39: nr: 0
39: Dih. Rest.:
39: nr: 0
39: Dih. Rest. Viol.:
39: nr: 0
39: Constraint:
39: nr: 0
39: Constr. No Conn.:
39: nr: 0
39: Settle:
39: nr: 0
39: Virtual site 2:
39: nr: 0
39: Virtual site 2fd:
39: nr: 0
39: Virtual site 3:
39: nr: 0
39: Virtual site 3fd:
39: nr: 0
39: Virtual site 3fad:
39: nr: 0
39: Virtual site 3out:
39: nr: 0
39: Virtual site 4fd:
39: nr: 0
39: Virtual site 4fdn:
39: nr: 0
39: Virtual site N:
39: nr: 0
39: COM Pull En.:
39: nr: 0
39: Density fitting:
39: nr: 0
39: Quantum En.:
39: nr: 0
39: Potential:
39: nr: 0
39: Kinetic En.:
39: nr: 0
39: Total Energy:
39: nr: 0
39: Conserved En.:
39: nr: 0
39: Temperature:
39: nr: 0
39: Vir. Temp. (not used):
39: nr: 0
39: Pres. DC:
39: nr: 0
39: Pressure:
39: nr: 0
39: dH/dl constr.:
39: nr: 0
39: dVremain/dl:
39: nr: 0
39: dEkin/dl:
39: nr: 0
39: dVcoul/dl:
39: nr: 0
39: dVvdw/dl:
39: nr: 0
39: dVbonded/dl:
39: nr: 0
39: dVrestraint/dl:
39: nr: 0
39: dVtemperature/dl:
39: nr: 0
39: grp[T-Coupling ] nr=1, name=[ rest]
39: grp[Energy Mon. ] nr=1, name=[ rest]
39: grp[Acceleration] nr=1, name=[ rest]
39: grp[Freeze ] nr=1, name=[ rest]
39: grp[User1 ] nr=1, name=[ rest]
39: grp[User2 ] nr=1, name=[ rest]
39: grp[VCM ] nr=1, name=[ rest]
39: grp[Compressed X] nr=1, name=[ rest]
39: grp[Or. Res. Fit] nr=1, name=[ rest]
39: grp[QMMM ] nr=1, name=[ rest]
39: grpname (11):
39: grpname[0]={name="System"}
39: grpname[1]={name="Protein"}
39: grpname[2]={name="Protein-H"}
39: grpname[3]={name="C-alpha"}
39: grpname[4]={name="Backbone"}
39: grpname[5]={name="MainChain"}
39: grpname[6]={name="MainChain+Cb"}
39: grpname[7]={name="MainChain+H"}
39: grpname[8]={name="SideChain"}
39: grpname[9]={name="SideChain-H"}
39: grpname[10]={name="rest"}
39: groups T-Cou Energ Accel Freez User1 User2 VCM Compr Or. R QMMM
39: allocated 0 0 0 0 0 0 0 0 0 0
39: groupnr[ *] = 0 0 0 0 0 0 0 0 0 0
39: box (3x3):
39: box[ 0]={ 5.90620e+00, 0.00000e+00, 0.00000e+00}
39: box[ 1]={ 0.00000e+00, 6.84510e+00, 0.00000e+00}
39: box[ 2]={ 0.00000e+00, 0.00000e+00, 3.05170e+00}
39: box_rel (3x3):
39: box_rel[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: box_rel[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv (3x3):
39: boxv[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: boxv[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev (3x3):
39: pres_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: pres_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev (3x3):
39: svir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: svir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev (3x3):
39: fvir_prev[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: fvir_prev[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: nosehoover_xi: not available
39: x (156x3):
39: x[ 0]={ 3.53600e+00, 2.23400e+00, -1.19800e+00}
39: x[ 1]={ 3.61200e+00, 2.28800e+00, -1.23600e+00}
39: x[ 2]={ 3.47000e+00, 2.21400e+00, -1.27000e+00}
39: x[ 3]={ 3.49200e+00, 2.28600e+00, -1.12500e+00}
39: x[ 4]={ 3.58900e+00, 2.10700e+00, -1.14300e+00}
39: x[ 5]={ 3.63300e+00, 2.05500e+00, -1.21600e+00}
39: x[ 6]={ 3.68700e+00, 2.14400e+00, -1.03100e+00}
39: x[ 7]={ 3.76300e+00, 2.19500e+00, -1.07000e+00}
39: x[ 8]={ 3.63900e+00, 2.20100e+00, -9.64000e-01}
39: x[ 9]={ 3.74500e+00, 2.02500e+00, -9.56000e-01}
39: x[ 10]={ 3.67600e+00, 1.98900e+00, -8.94000e-01}
39: x[ 11]={ 3.77000e+00, 1.95400e+00, -1.02300e+00}
39: x[ 12]={ 3.86900e+00, 2.06500e+00, -8.77000e-01}
39: x[ 13]={ 3.94500e+00, 2.08300e+00, -9.40000e-01}
39: x[ 14]={ 3.84900e+00, 2.14700e+00, -8.24000e-01}
39: x[ 15]={ 3.90600e+00, 1.95100e+00, -7.84000e-01}
39: x[ 16]={ 3.84100e+00, 1.94600e+00, -7.08000e-01}
39: x[ 17]={ 3.90600e+00, 1.86400e+00, -8.33000e-01}
39: x[ 18]={ 4.04200e+00, 1.97700e+00, -7.30000e-01}
39: x[ 19]={ 4.06900e+00, 1.90300e+00, -6.68000e-01}
39: x[ 20]={ 4.10800e+00, 1.98200e+00, -8.06000e-01}
39: x[ 21]={ 4.04200e+00, 2.06400e+00, -6.80000e-01}
39: x[ 22]={ 3.47400e+00, 2.02600e+00, -1.08400e+00}
39: x[ 23]={ 3.39500e+00, 2.08100e+00, -1.00800e+00}
39: x[ 24]={ 3.47400e+00, 1.89600e+00, -1.10400e+00}
39: x[ 25]={ 3.53600e+00, 1.86000e+00, -1.17400e+00}
39: x[ 26]={ 3.39000e+00, 1.80000e+00, -1.03300e+00}
39: x[ 27]={ 3.31700e+00, 1.85200e+00, -9.90000e-01}
39: x[ 28]={ 3.31400e+00, 1.70300e+00, -1.12300e+00}
39: x[ 29]={ 3.38600e+00, 1.65200e+00, -1.17000e+00}
39: x[ 30]={ 3.22500e+00, 1.60800e+00, -1.04300e+00}
39: x[ 31]={ 3.17700e+00, 1.54700e+00, -1.10600e+00}
39: x[ 32]={ 3.28200e+00, 1.55500e+00, -9.81000e-01}
39: x[ 33]={ 3.15800e+00, 1.66100e+00, -9.91000e-01}
39: x[ 34]={ 3.22900e+00, 1.77100e+00, -1.22900e+00}
39: x[ 35]={ 3.18300e+00, 1.70200e+00, -1.28400e+00}
39: x[ 36]={ 3.16200e+00, 1.83000e+00, -1.18500e+00}
39: x[ 37]={ 3.28800e+00, 1.82700e+00, -1.28800e+00}
39: x[ 38]={ 3.48000e+00, 1.73100e+00, -9.29000e-01}
39: x[ 39]={ 3.57600e+00, 1.66100e+00, -9.66000e-01}
39: x[ 40]={ 3.44900e+00, 1.75500e+00, -8.04000e-01}
39: x[ 41]={ 3.37500e+00, 1.81900e+00, -7.84000e-01}
39: x[ 42]={ 3.51900e+00, 1.69000e+00, -6.92000e-01}
39: x[ 43]={ 3.61500e+00, 1.69700e+00, -7.17000e-01}
39: x[ 44]={ 3.49700e+00, 1.76300e+00, -5.59000e-01}
39: x[ 45]={ 3.40500e+00, 1.80200e+00, -5.58000e-01}
39: x[ 46]={ 3.50600e+00, 1.69800e+00, -4.84000e-01}
39: x[ 47]={ 3.59400e+00, 1.87400e+00, -5.38000e-01}
39: x[ 48]={ 3.56700e+00, 2.00500e+00, -5.80000e-01}
39: x[ 49]={ 3.48100e+00, 2.02500e+00, -6.27000e-01}
39: x[ 50]={ 3.70000e+00, 1.85600e+00, -4.47000e-01}
39: x[ 51]={ 3.71300e+00, 1.76600e+00, -4.05000e-01}
39: x[ 52]={ 3.65800e+00, 2.10800e+00, -5.57000e-01}
39: x[ 53]={ 3.64800e+00, 2.19500e+00, -6.04000e-01}
39: x[ 54]={ 3.78700e+00, 1.95900e+00, -4.16000e-01}
39: x[ 55]={ 3.86600e+00, 1.94200e+00, -3.57000e-01}
39: x[ 56]={ 3.76400e+00, 2.08700e+00, -4.67000e-01}
39: x[ 57]={ 3.82200e+00, 2.16400e+00, -4.39000e-01}
39: x[ 58]={ 3.47400e+00, 1.54400e+00, -6.77000e-01}
39: x[ 59]={ 3.35200e+00, 1.51600e+00, -6.86000e-01}
39: x[ 60]={ 3.57200e+00, 1.46400e+00, -6.33000e-01}
39: x[ 61]={ 3.66700e+00, 1.49500e+00, -6.32000e-01}
39: x[ 62]={ 3.53700e+00, 1.32800e+00, -5.87000e-01}
39: x[ 63]={ 3.46200e+00, 1.29200e+00, -6.43000e-01}
39: x[ 64]={ 3.61600e+00, 1.26800e+00, -5.94000e-01}
39: x[ 65]={ 3.49200e+00, 1.34200e+00, -4.42000e-01}
39: x[ 66]={ 3.53000e+00, 1.44000e+00, -3.78000e-01}
39: x[ 67]={ 3.40500e+00, 1.25400e+00, -3.97000e-01}
39: x[ 68]={ 3.37100e+00, 1.18400e+00, -4.60000e-01}
39: x[ 69]={ 3.35600e+00, 1.25400e+00, -2.59000e-01}
39: x[ 70]={ 3.29800e+00, 1.33400e+00, -2.52000e-01}
39: x[ 71]={ 3.27600e+00, 1.12600e+00, -2.33000e-01}
39: x[ 72]={ 3.20000e+00, 1.12200e+00, -2.97000e-01}
39: x[ 73]={ 3.33600e+00, 1.04700e+00, -2.47000e-01}
39: x[ 74]={ 3.22100e+00, 1.12000e+00, -9.20000e-02}
39: x[ 75]={ 3.29700e+00, 1.11700e+00, -2.70000e-02}
39: x[ 76]={ 3.16500e+00, 1.20100e+00, -7.50000e-02}
39: x[ 77]={ 3.13800e+00, 1.00000e+00, -7.20000e-02}
39: x[ 78]={ 3.10400e+00, 9.99000e-01, 2.20000e-02}
39: x[ 79]={ 3.06000e+00, 1.00500e+00, -1.35000e-01}
39: x[ 80]={ 3.20600e+00, 8.75000e-01, -9.60000e-02}
39: x[ 81]={ 3.20200e+00, 8.40000e-01, -1.89000e-01}
39: x[ 82]={ 3.27300e+00, 8.01000e-01, -1.00000e-02}
39: x[ 83]={ 3.28400e+00, 8.33000e-01, 1.19000e-01}
39: x[ 84]={ 3.23900e+00, 9.16000e-01, 1.53000e-01}
39: x[ 85]={ 3.33600e+00, 7.75000e-01, 1.81000e-01}
39: x[ 86]={ 3.32500e+00, 6.84000e-01, -5.30000e-02}
39: x[ 87]={ 3.31100e+00, 6.55000e-01, -1.47000e-01}
39: x[ 88]={ 3.37600e+00, 6.26000e-01, 1.00000e-02}
39: x[ 89]={ 3.46700e+00, 1.27300e+00, -1.56000e-01}
39: x[ 90]={ 3.46700e+00, 1.36500e+00, -7.00000e-02}
39: x[ 91]={ 3.56700e+00, 1.18500e+00, -1.61000e-01}
39: x[ 92]={ 3.56700e+00, 1.11600e+00, -2.33000e-01}
39: x[ 93]={ 3.67800e+00, 1.18700e+00, -6.50000e-02}
39: x[ 94]={ 3.63100e+00, 1.20200e+00, 2.20000e-02}
39: x[ 95]={ 3.74900e+00, 1.05300e+00, -6.20000e-02}
39: x[ 96]={ 3.77000e+00, 1.03400e+00, -1.58000e-01}
39: x[ 97]={ 3.83400e+00, 1.07200e+00, -1.30000e-02}
39: x[ 98]={ 3.65400e+00, 9.20000e-01, 1.40000e-02}
39: x[ 99]={ 3.70750e+00, 8.35500e-01, 1.20000e-02}
39: x[ 100]={ 3.77500e+00, 1.30500e+00, -7.80000e-02}
39: x[ 101]={ 3.81500e+00, 1.36100e+00, 2.60000e-02}
39: x[ 102]={ 3.78600e+00, 1.34800e+00, -2.02000e-01}
39: x[ 103]={ 3.74000e+00, 1.30000e+00, -2.76000e-01}
39: x[ 104]={ 3.86800e+00, 1.46900e+00, -2.31000e-01}
39: x[ 105]={ 3.96000e+00, 1.45500e+00, -1.93000e-01}
39: x[ 106]={ 3.87800e+00, 1.48500e+00, -3.82000e-01}
39: x[ 107]={ 3.92300e+00, 1.40200e+00, -4.17000e-01}
39: x[ 108]={ 3.78500e+00, 1.48900e+00, -4.17000e-01}
39: x[ 109]={ 3.95400e+00, 1.60500e+00, -4.38000e-01}
39: x[ 110]={ 3.91300e+00, 1.68700e+00, -3.99000e-01}
39: x[ 111]={ 4.04900e+00, 1.59800e+00, -4.07000e-01}
39: x[ 112]={ 3.95800e+00, 1.62400e+00, -5.87000e-01}
39: x[ 113]={ 3.86700e+00, 1.56400e+00, -6.49000e-01}
39: x[ 114]={ 4.04200e+00, 1.69500e+00, -6.38000e-01}
39: x[ 115]={ 3.80500e+00, 1.59300e+00, -1.66000e-01}
39: x[ 116]={ 3.87400e+00, 1.67300e+00, -1.01000e-01}
39: x[ 117]={ 3.67400e+00, 1.60500e+00, -1.82000e-01}
39: x[ 118]={ 3.62600e+00, 1.53500e+00, -2.35000e-01}
39: x[ 119]={ 3.59600e+00, 1.71600e+00, -1.25000e-01}
39: x[ 120]={ 3.64000e+00, 1.80100e+00, -1.56000e-01}
39: x[ 121]={ 3.45300e+00, 1.71700e+00, -1.81000e-01}
39: x[ 122]={ 3.45700e+00, 1.72200e+00, -2.81000e-01}
39: x[ 123]={ 3.40600e+00, 1.63300e+00, -1.53000e-01}
39: x[ 124]={ 3.37200e+00, 1.83500e+00, -1.31000e-01}
39: x[ 125]={ 3.37800e+00, 1.84200e+00, -3.10000e-02}
39: x[ 126]={ 3.43000e+00, 1.96600e+00, -1.84000e-01}
39: x[ 127]={ 3.37600e+00, 2.04300e+00, -1.50000e-01}
39: x[ 128]={ 3.52400e+00, 1.97500e+00, -1.53000e-01}
39: x[ 129]={ 3.42700e+00, 1.96500e+00, -2.84000e-01}
39: x[ 130]={ 3.22500e+00, 1.81400e+00, -1.60000e-01}
39: x[ 131]={ 3.17200e+00, 1.89300e+00, -1.26000e-01}
39: x[ 132]={ 3.21100e+00, 1.80500e+00, -2.58000e-01}
39: x[ 133]={ 3.19300e+00, 1.73100e+00, -1.14000e-01}
39: x[ 134]={ 3.60500e+00, 1.71300e+00, 2.70000e-02}
39: x[ 135]={ 3.61600e+00, 1.81700e+00, 9.20000e-02}
39: x[ 136]={ 3.57500e+00, 1.59800e+00, 8.30000e-02}
39: x[ 137]={ 3.54600e+00, 1.52200e+00, 2.40000e-02}
39: x[ 138]={ 3.58400e+00, 1.57600e+00, 2.28000e-01}
39: x[ 139]={ 3.50800e+00, 1.62600e+00, 2.69000e-01}
39: x[ 140]={ 3.56600e+00, 1.42900e+00, 2.62000e-01}
39: x[ 141]={ 3.57200e+00, 1.41600e+00, 3.61000e-01}
39: x[ 142]={ 3.47600e+00, 1.39800e+00, 2.30000e-01}
39: x[ 143]={ 3.63700e+00, 1.37500e+00, 2.18000e-01}
39: x[ 144]={ 3.71400e+00, 1.63100e+00, 2.84000e-01}
39: x[ 145]={ 3.71500e+00, 1.69800e+00, 3.90000e-01}
39: x[ 146]={ 3.82700e+00, 1.59800e+00, 2.20000e-01}
39: x[ 147]={ 3.82000e+00, 1.53900e+00, 1.40000e-01}
39: x[ 148]={ 3.96100e+00, 1.64300e+00, 2.62000e-01}
39: x[ 149]={ 3.96900e+00, 1.61900e+00, 3.58000e-01}
39: x[ 150]={ 4.07100e+00, 1.57100e+00, 1.84000e-01}
39: x[ 151]={ 4.16000e+00, 1.60300e+00, 2.15000e-01}
39: x[ 152]={ 4.06400e+00, 1.47200e+00, 2.01000e-01}
39: x[ 153]={ 4.06000e+00, 1.58900e+00, 8.60000e-02}
39: x[ 154]={ 3.97400e+00, 1.79400e+00, 2.46000e-01}
39: x[ 155]={ 4.01900e+00, 1.85000e+00, 3.47000e-01}
39: v (156x3):
39: v[ 0]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 1]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 2]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 3]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 4]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 5]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 6]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 7]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 8]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 9]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 10]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 11]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 12]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 13]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 14]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 15]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 16]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 17]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 18]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 19]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 20]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 21]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 22]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 23]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 24]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 25]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 26]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 27]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 28]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 29]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 30]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 31]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 32]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 33]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 34]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 35]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 36]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 37]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 38]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 39]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 40]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 41]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 42]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 43]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 44]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 45]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 46]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 47]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 48]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 49]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 50]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 51]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 52]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 53]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 54]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 55]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 56]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 57]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 58]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 59]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 60]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 61]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 62]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 63]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 64]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 65]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 66]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 67]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 68]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 69]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 70]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 71]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 72]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 73]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 74]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 75]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 76]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 77]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 78]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 79]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 80]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 81]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 82]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 83]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 84]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 85]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 86]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 87]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 88]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 89]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 90]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 91]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 92]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 93]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 94]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 95]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 96]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 97]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 98]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 99]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 100]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 101]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 102]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 103]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 104]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 105]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 106]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 107]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 108]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 109]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 110]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 111]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 112]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 113]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 114]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 115]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 116]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 117]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 118]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 119]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 120]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 121]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 122]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 123]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 124]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 125]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 126]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 127]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 128]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 129]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 130]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 131]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 132]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 133]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 134]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 135]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 136]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 137]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 138]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 139]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 140]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 141]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 142]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 143]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 144]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 145]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 146]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 147]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 148]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 149]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 150]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 151]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 152]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 153]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 154]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: v[ 155]={ 0.00000e+00, 0.00000e+00, 0.00000e+00}
39: Group statistics
39: T-Coupling : 156 (total 156 atoms)
39: Energy Mon. : 156 (total 156 atoms)
39: Acceleration: 156 (total 156 atoms)
39: Freeze : 156 (total 156 atoms)
39: User1 : 156 (total 156 atoms)
39: User2 : 156 (total 156 atoms)
39: VCM : 156 (total 156 atoms)
39: Compressed X: 156 (total 156 atoms)
39: Or. Res. Fit: 156 (total 156 atoms)
39: QMMM : 156 (total 156 atoms)
39: [ OK ] DumpTest.WorksWithTpr (45 ms)
39: [ RUN ] DumpTest.WorksWithTprAndMdpWriting
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/DumpTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
39: [ OK ] DumpTest.WorksWithTprAndMdpWriting (7 ms)
39: [----------] 2 tests from DumpTest (53 ms total)
39:
39: [----------] 4 tests from ReportMethodsTest
39:
39: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: For a correct single-point energy evaluation with nsteps = 0, use
39: continuation = yes to avoid constraining the input coordinates.
39:
39: Setting the LD random seed to -34611343
39: Generated 330891 of the 330891 non-bonded parameter combinations
39: Generating 1-4 interactions: fudge = 0.5
39: Generated 330891 of the 330891 1-4 parameter combinations
39: Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
39:
39: NOTE 2 [file lysozyme.top, line 1465]:
39: System has non-zero total charge: 2.000000
39: Total charge should normally be an integer. See
39: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
39: for discussion on how close it should be to an integer.
39:
39:
39:
39: Number of degrees of freedom in T-Coupling group rest is 465.00
39:
39: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: NVE simulation with an initial temperature of zero: will use a Verlet
39: buffer of 10%. Check your energy drift!
39:
39:
39: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.mdp]:
39: You are using a plain Coulomb cut-off, which might produce artifacts.
39: You might want to consider using PME electrostatics.
39:
39:
39:
39: There were 4 notes
39: Analysing residue names:
39: There are: 10 Protein residues
39: Analysing Protein...
39: This run will generate roughly 0 Mb of data
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersFormated
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersFormated (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectHeadersUnformatted
39: [ OK ] ReportMethodsTest.WritesCorrectHeadersUnformatted (0 ms)
39: [ RUN ] ReportMethodsTest.WritesCorrectInformation
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
39: [ OK ] ReportMethodsTest.WritesCorrectInformation (5 ms)
39: [ RUN ] ReportMethodsTest.ToolEndToEndTest
39: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/gromacs/tools/tests/Testing/Temporary/ReportMethodsTest_lysozyme.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
39: section: Methods
39: subsection: Simulation system
39: A system of 1 molecules (156 atoms) was simulated.
39:
39: subsection: Simulation settings
39: A total of 0 ns were simulated with a time step of 1 fs.
39: Neighbor searching was performed every 10 steps.
39: The Cut-off algorithm was used for electrostatic interactions.
39: with a cut-off of 1 nm.
39: A single cut-off of 1.1 nm was used for Van der Waals interactions.
39: [ OK ] ReportMethodsTest.ToolEndToEndTest (5 ms)
39: [----------] 4 tests from ReportMethodsTest (10 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: trr version: GMX_trn_file (single precision)
39:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/0 (14 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/1 (15 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/2 (13 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/3 (14 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/4 (13 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5
39: Will write tng: Trajectory file (tng format)
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset.WithDifferentInputFormats/5 (14 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithIndexGroupSubset (83 ms total)
39:
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/0 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.tng is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/1 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/2 (3 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from gro file '', 6 atoms.
39:
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.gro is 0.001 (nm)
39: -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/3 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group: Reading frames from pdb file
Reading frame 0 time 0.000
39: Precision of /<<PKGBUILDDIR>>/src/testutils/simulationdatabase/spc2-traj.pdb is 0.0001 (nm)
39: -> frame 0 time 0.000
't= 0.00000', 6 atoms
39:
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/4 (4 ms)
39: [ RUN ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5
39: Will write trr: Trajectory in portable xdr format
39: Group 0 ( System) has 6 elements
39: Group 1 (FirstWaterMolecule) has 3 elements
39: Group 2 (SecondWaterMolecule) has 3 elements
39: Select a group:
Reading frame 0 time 0.000 -> frame 0 time 0.000
Reading frame 1 time 0.000 -> frame 1 time 0.000
Last frame 1 time 0.000
39:
39: Note that major changes are planned in future for trjconv, to improve usability and utility.
39: Select group for output
39: Selected 2: 'SecondWaterMolecule'
39: [ OK ] NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile.WithDifferentInputFormats/5 (4 ms)
39: [----------] 6 tests from NoFatalErrorWhenWritingFrom/TrjconvWithoutTopologyFile (24 ms total)
39:
39: [----------] Global test environment tear-down
39: [==========] 18 tests from 4 test cases ran. (9051 ms total)
39: [ PASSED ] 18 tests.
39/54 Test #39: ToolUnitTests ....................... Passed 9.13 sec
test 40
Start 40: FileIOTests
40: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/fileio-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/FileIOTests.xml"
40: Test timeout computed to be: 30
40: [==========] Running 33 tests from 8 test cases.
40: [----------] Global test environment set-up.
40: [----------] 2 tests from FileMD5Test
40: [ RUN ] FileMD5Test.CanComputeMD5
40: [ OK ] FileMD5Test.CanComputeMD5 (4 ms)
40: [ RUN ] FileMD5Test.ReturnsErrorIfFileModeIsWrong
40: [ OK ] FileMD5Test.ReturnsErrorIfFileModeIsWrong (1 ms)
40: [----------] 2 tests from FileMD5Test (6 ms total)
40:
40: [----------] 3 tests from MrcSerializer
40: [ RUN ] MrcSerializer.DefaultHeaderValuesAreSet
40: [ OK ] MrcSerializer.DefaultHeaderValuesAreSet (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderHasRightSerialSize
40: [ OK ] MrcSerializer.DefaultHeaderHasRightSerialSize (0 ms)
40: [ RUN ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip
40: [ OK ] MrcSerializer.DefaultHeaderIdenticalAfterRoundTrip (5 ms)
40: [----------] 3 tests from MrcSerializer (5 ms total)
40:
40: [----------] 4 tests from MrcDensityMap
40: [ RUN ] MrcDensityMap.RoundTripIsIdempotent
40: [ OK ] MrcDensityMap.RoundTripIsIdempotent (4 ms)
40: [ RUN ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent
40: [ OK ] MrcDensityMap.ThrowsFileIOErrorWhenFileNotPresent (0 ms)
40: [ RUN ] MrcDensityMap.ReadsCoordinateTransformationFromFile
40: [ OK ] MrcDensityMap.ReadsCoordinateTransformationFromFile (1 ms)
40: [ RUN ] MrcDensityMap.ReadsDensityDataFromFile
40: [ OK ] MrcDensityMap.ReadsDensityDataFromFile (34 ms)
40: [----------] 4 tests from MrcDensityMap (41 ms total)
40:
40: [----------] 8 tests from MrcDensityMapHeaderTest
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsZeroForDefaultHeader (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeIsCorrect
40: [ OK ] MrcDensityMapHeaderTest.DataSizeIsCorrect (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid
40: [ OK ] MrcDensityMapHeaderTest.DataSizeThrowsWhenInvalid (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformNoOriginGiven (1 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithOriginDefined (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectCoordinateTransformWithStartValues (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.GetsCorrectExtents
40: [ OK ] MrcDensityMapHeaderTest.GetsCorrectExtents (0 ms)
40: [ RUN ] MrcDensityMapHeaderTest.IsSane
40: [ OK ] MrcDensityMapHeaderTest.IsSane (0 ms)
40: [----------] 8 tests from MrcDensityMapHeaderTest (1 ms total)
40:
40: [----------] 9 tests from ReadTest
40: [ RUN ] ReadTest.get_eint_ReadsInteger
40: [ OK ] ReadTest.get_eint_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_eint64_ReadsInteger
40: [ OK ] ReadTest.get_eint64_ReadsInteger (1 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutFloat
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side '0.8' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutFloat (0 ms)
40: [ RUN ] ReadTest.get_eint64_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not an
40: integer value
40:
40:
40: [ OK ] ReadTest.get_eint64_WarnsAboutString (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsInteger
40: [ OK ] ReadTest.get_ereal_ReadsInteger (0 ms)
40: [ RUN ] ReadTest.get_ereal_ReadsFloat
40: [ OK ] ReadTest.get_ereal_ReadsFloat (0 ms)
40: [ RUN ] ReadTest.get_ereal_WarnsAboutString
40:
40: ERROR 1 [file unknown, line 0]:
40: Right hand side 'hello' for parameter 'test' in parameter file is not a
40: real value
40:
40:
40: [ OK ] ReadTest.get_ereal_WarnsAboutString (0 ms)
40: [----------] 9 tests from ReadTest (1 ms total)
40:
40: [----------] 1 test from FileIOXdrSerializerTest
40: [ RUN ] FileIOXdrSerializerTest.SizeIsCorrect
40: [ OK ] FileIOXdrSerializerTest.SizeIsCorrect (1 ms)
40: [----------] 1 test from FileIOXdrSerializerTest (1 ms total)
40:
40: [----------] 2 tests from TngTest
40: [ RUN ] TngTest.CanOpenTngFile
40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
40: TNG library: Cannot open file spc2-traj.tng. ./src/external/tng_io/src/lib/tng_io.c: 890
40: [ OK ] TngTest.CanOpenTngFile (1 ms)
40: [ RUN ] TngTest.CloseBeforeOpenIsNotFatal
40: [ OK ] TngTest.CloseBeforeOpenIsNotFatal (0 ms)
40: [----------] 2 tests from TngTest (1 ms total)
40:
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/0 (3 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/1 (3 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/2 (9 ms)
40: [ RUN ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3
40: [ OK ] WithDifferentFormats/StructureIORoundtripTest.ReadWriteTpsConf/3 (2 ms)
40: [----------] 4 tests from WithDifferentFormats/StructureIORoundtripTest (17 ms total)
40:
40: [----------] Global test environment tear-down
40: [==========] 33 tests from 8 test cases ran. (73 ms total)
40: [ PASSED ] 33 tests.
40/54 Test #40: FileIOTests ......................... Passed 0.14 sec
test 41
Start 41: SelectionUnitTests
41: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/selection-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/SelectionUnitTests.xml"
41: Test timeout computed to be: 30
41: [==========] Running 192 tests from 11 test cases.
41: [----------] Global test environment set-up.
41: [----------] 1 test from IndexGroupTest
41: [ RUN ] IndexGroupTest.RemovesDuplicates
41: [ OK ] IndexGroupTest.RemovesDuplicates (0 ms)
41: [----------] 1 test from IndexGroupTest (0 ms total)
41:
41: [----------] 15 tests from IndexBlockTest
41: [ RUN ] IndexBlockTest.CreatesUnknownBlock
41: [ OK ] IndexBlockTest.CreatesUnknownBlock (1 ms)
41: [ RUN ] IndexBlockTest.CreatesAtomBlock
41: [ OK ] IndexBlockTest.CreatesAtomBlock (1 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForSimpleTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesResidueBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesResidueBlocksForComplexTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForSimpleTopology (0 ms)
41: [ RUN ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology
41: [ OK ] IndexBlockTest.CreatesMoleculeBlocksForComplexTopology (1 ms)
41: [ RUN ] IndexBlockTest.CreatesSingleBlock
41: [ OK ] IndexBlockTest.CreatesSingleBlock (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksPositive (1 ms)
41: [ RUN ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive
41: [ OK ] IndexBlockTest.ChecksOutOfOrderGroupForFullBlocksPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForFullBlocksNegative
41: [ OK ] IndexBlockTest.ChecksGroupForFullBlocksNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteElementsTrivial (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesPositive (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteResiduesNegative (0 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesPositive (1 ms)
41: [ RUN ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative
41: [ OK ] IndexBlockTest.ChecksGroupForCompleteMoleculesNegative (0 ms)
41: [----------] 15 tests from IndexBlockTest (9 ms total)
41:
41: [----------] 11 tests from IndexMapTest
41: [ RUN ] IndexMapTest.InitializesAtomBlock
41: [ OK ] IndexMapTest.InitializesAtomBlock (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAtom
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAtom (0 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupSingle
41: [ OK ] IndexMapTest.InitializesOrgIdGroupSingle (1 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupResidue
41: [ OK ] IndexMapTest.InitializesOrgIdGroupResidue (1 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupMolecule
41: [ OK ] IndexMapTest.InitializesOrgIdGroupMolecule (1 ms)
41: [ RUN ] IndexMapTest.InitializesOrgIdGroupAll
41: [ OK ] IndexMapTest.InitializesOrgIdGroupAll (0 ms)
41: [ RUN ] IndexMapTest.InitializesMoleculeBlock
41: [ OK ] IndexMapTest.InitializesMoleculeBlock (0 ms)
41: [ RUN ] IndexMapTest.MapsSingleBlock
41: [ OK ] IndexMapTest.MapsSingleBlock (1 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocks
41: [ OK ] IndexMapTest.MapsResidueBlocks (1 ms)
41: [ RUN ] IndexMapTest.MapsResidueBlocksWithMask
41: [ OK ] IndexMapTest.MapsResidueBlocksWithMask (2 ms)
41: [ RUN ] IndexMapTest.HandlesMultipleRequests
41: [ OK ] IndexMapTest.HandlesMultipleRequests (10 ms)
41: [----------] 11 tests from IndexMapTest (19 ms total)
41:
41: [----------] 3 tests from IndexGroupsAndNamesTest
41: [ RUN ] IndexGroupsAndNamesTest.containsNames
41: [ OK ] IndexGroupsAndNamesTest.containsNames (1 ms)
41: [ RUN ] IndexGroupsAndNamesTest.throwsWhenNameMissing
41: [ OK ] IndexGroupsAndNamesTest.throwsWhenNameMissing (1 ms)
41: [ RUN ] IndexGroupsAndNamesTest.groupIndicesCorrect
41: [ OK ] IndexGroupsAndNamesTest.groupIndicesCorrect (0 ms)
41: [----------] 3 tests from IndexGroupsAndNamesTest (2 ms total)
41:
41: [----------] 15 tests from NeighborhoodSearchTest
41: [ RUN ] NeighborhoodSearchTest.SimpleSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSearch (76 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchXY
41: [ OK ] NeighborhoodSearchTest.SimpleSearchXY (76 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchBox
41: [ OK ] NeighborhoodSearchTest.GridSearchBox (13 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchTriclinic
41: [ OK ] NeighborhoodSearchTest.GridSearchTriclinic (49 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearch2DPBC
41: [ OK ] NeighborhoodSearchTest.GridSearch2DPBC (25 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchNoPBC
41: [ OK ] NeighborhoodSearchTest.GridSearchNoPBC (14 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchXYBox
41: [ OK ] NeighborhoodSearchTest.GridSearchXYBox (14 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.SimpleSelfPairsSearch (1 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSelfPairsSearch
41: [ OK ] NeighborhoodSearchTest.GridSelfPairsSearch (218 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesConcurrentSearches
41: [ OK ] NeighborhoodSearchTest.HandlesConcurrentSearches (1 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNoPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNoPBC (0 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesNullPBC
41: [ OK ] NeighborhoodSearchTest.HandlesNullPBC (1 ms)
41: [ RUN ] NeighborhoodSearchTest.HandlesSkippingPairs
41: [ OK ] NeighborhoodSearchTest.HandlesSkippingPairs (0 ms)
41: [ RUN ] NeighborhoodSearchTest.SimpleSearchExclusions
41: [ OK ] NeighborhoodSearchTest.SimpleSearchExclusions (18 ms)
41: [ RUN ] NeighborhoodSearchTest.GridSearchExclusions
41: [ OK ] NeighborhoodSearchTest.GridSearchExclusions (4 ms)
41: [----------] 15 tests from NeighborhoodSearchTest (512 ms total)
41:
41: [----------] 12 tests from PositionCalculationTest
41: [ RUN ] PositionCalculationTest.ComputesAtomPositions
41: [ OK ] PositionCalculationTest.ComputesAtomPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOGPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOGPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesResidueCOMPositions
41: [ OK ] PositionCalculationTest.ComputesResidueCOMPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOGPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOGPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesGroupCOMPositions
41: [ OK ] PositionCalculationTest.ComputesGroupCOMPositions (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteWhole
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteWhole (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionsWithCompleteMax
41: [ OK ] PositionCalculationTest.ComputesPositionsWithCompleteMax (1 ms)
41: [ RUN ] PositionCalculationTest.ComputesPositionMask
41: [ OK ] PositionCalculationTest.ComputesPositionMask (2 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesFramesWithLessAtoms2
41: [ OK ] PositionCalculationTest.HandlesFramesWithLessAtoms2 (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesIdenticalStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesIdenticalStaticCalculations (1 ms)
41: [ RUN ] PositionCalculationTest.HandlesOverlappingStaticCalculations
41: [ OK ] PositionCalculationTest.HandlesOverlappingStaticCalculations (2 ms)
41: [----------] 12 tests from PositionCalculationTest (17 ms total)
41:
41: [----------] 29 tests from SelectionCollectionTest
41: [ RUN ] SelectionCollectionTest.HandlesNoSelections
41: [ OK ] SelectionCollectionTest.HandlesNoSelections (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType
41: [ OK ] SelectionCollectionTest.HandlesNoSelectionsWithDefaultPositionType (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesVelocityAndForceRequests
41: [ OK ] SelectionCollectionTest.HandlesVelocityAndForceRequests (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry
41: [ OK ] SelectionCollectionTest.HandlesForceRequestForCenterOfGeometry (2 ms)
41: [ RUN ] SelectionCollectionTest.ParsesSelectionsFromFile
41: [ OK ] SelectionCollectionTest.ParsesSelectionsFromFile (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesAtypicalWhitespace
41: [ OK ] SelectionCollectionTest.HandlesAtypicalWhitespace (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesInvalidRegularExpressions
41: [ OK ] SelectionCollectionTest.HandlesInvalidRegularExpressions (3 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue2
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesMissingMethodParamValue3
41: [ OK ] SelectionCollectionTest.HandlesMissingMethodParamValue3 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser1 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceParser2 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed1 (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2
41: [ OK ] SelectionCollectionTest.HandlesUnknownGroupReferenceDelayed2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReference
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReference (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed
41: [ OK ] SelectionCollectionTest.HandlesUnsortedGroupReferenceDelayed (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroup (1 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2
41: [ OK ] SelectionCollectionTest.HandlesOutOfRangeAtomIndexInGroupDelayed2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingMoleculeInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingAtomTypes
41: [ OK ] SelectionCollectionTest.RecoversFromMissingAtomTypes (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromMissingPDBInfo
41: [ OK ] SelectionCollectionTest.RecoversFromMissingPDBInfo (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation (2 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation2
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation2 (1 ms)
41: [ RUN ] SelectionCollectionTest.RecoversFromInvalidPermutation3
41: [ OK ] SelectionCollectionTest.RecoversFromInvalidPermutation3 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets2 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets3 (2 ms)
41: [ RUN ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4
41: [ OK ] SelectionCollectionTest.HandlesFramesWithTooSmallAtomSubsets4 (2 ms)
41: [----------] 29 tests from SelectionCollectionTest (52 ms total)
41:
41: [----------] 14 tests from SelectionCollectionInteractiveTest
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesBasicInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesBasicInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesContinuation
41: [ OK ] SelectionCollectionInteractiveTest.HandlesContinuation (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithGroups (4 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesStatusWithExistingSelections (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputStatus (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesTwoSelectionInputStatus (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultiSelectionInputStatus (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoFinalNewline (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesEmptySelections
41: [ OK ] SelectionCollectionInteractiveTest.HandlesEmptySelections (3 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine
41: [ OK ] SelectionCollectionInteractiveTest.HandlesMultipleSelectionsOnLine (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput
41: [ OK ] SelectionCollectionInteractiveTest.HandlesNoninteractiveInput (2 ms)
41: [ RUN ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively
41: [ OK ] SelectionCollectionInteractiveTest.HandlesSingleSelectionInputNoninteractively (1 ms)
41: [----------] 14 tests from SelectionCollectionInteractiveTest (35 ms total)
41:
41: [----------] 66 tests from SelectionCollectionDataTest
41: [ RUN ] SelectionCollectionDataTest.HandlesAllNone
41: [ OK ] SelectionCollectionDataTest.HandlesAllNone (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomnr
41: [ OK ] SelectionCollectionDataTest.HandlesAtomnr (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResnr
41: [ OK ] SelectionCollectionDataTest.HandlesResnr (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResIndex
41: [ OK ] SelectionCollectionDataTest.HandlesResIndex (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMolIndex
41: [ OK ] SelectionCollectionDataTest.HandlesMolIndex (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesAtomname (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPdbAtomname
41: [ OK ] SelectionCollectionDataTest.HandlesPdbAtomname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAtomtype
41: [ OK ] SelectionCollectionDataTest.HandlesAtomtype (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesChain
41: [ OK ] SelectionCollectionDataTest.HandlesChain (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMass
41: [ OK ] SelectionCollectionDataTest.HandlesMass (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCharge
41: [ OK ] SelectionCollectionDataTest.HandlesCharge (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesAltLoc
41: [ OK ] SelectionCollectionDataTest.HandlesAltLoc (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInsertCode
41: [ OK ] SelectionCollectionDataTest.HandlesInsertCode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOccupancy
41: [ OK ] SelectionCollectionDataTest.HandlesOccupancy (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBeta
41: [ OK ] SelectionCollectionDataTest.HandlesBeta (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesResname
41: [ OK ] SelectionCollectionDataTest.HandlesResname (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesCoordinateKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesCoordinateKeywords (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidue
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidue (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSameResidueName
41: [ OK ] SelectionCollectionDataTest.HandlesSameResidueName (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionKeywords (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesDistanceKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMinDistanceKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesMinDistanceKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesWithinKeyword (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword
41: [ OK ] SelectionCollectionDataTest.HandlesInSolidAngleKeyword (26 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPermuteModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPermuteModifier (10 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPlusModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPlusModifier (11 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesMergeModifier
41: [ OK ] SelectionCollectionDataTest.HandlesMergeModifier (12 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndCharges
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndCharges (9 ms)
41: [ RUN ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology
41: [ OK ] SelectionCollectionDataTest.ComputesMassesAndChargesWithoutTopology (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets
41: [ OK ] SelectionCollectionDataTest.HandlesFramesWithAtomSubsets (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesSelectionNames
41: [ OK ] SelectionCollectionDataTest.HandlesSelectionNames (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelections (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesIndexGroupsInSelectionsDelayed (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelections (9 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed
41: [ OK ] SelectionCollectionDataTest.HandlesUnsortedIndexGroupsInSelectionsDelayed (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositions (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionsWithModifiers (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWithinConstantPositions
41: [ OK ] SelectionCollectionDataTest.HandlesWithinConstantPositions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingIntegerRanges (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesOverlappingRealRanges
41: [ OK ] SelectionCollectionDataTest.HandlesOverlappingRealRanges (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode
41: [ OK ] SelectionCollectionDataTest.HandlesForcedStringMatchingMode (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesWildcardMatching
41: [ OK ] SelectionCollectionDataTest.HandlesWildcardMatching (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesRegexMatching
41: [ OK ] SelectionCollectionDataTest.HandlesRegexMatching (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBasicBoolean
41: [ OK ] SelectionCollectionDataTest.HandlesBasicBoolean (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters
41: [ OK ] SelectionCollectionDataTest.HandlesDynamicAtomValuedParameters (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesEmptySelectionWithUnevaluatedExpressions (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame
41: [ OK ] SelectionCollectionDataTest.HandlesEmptyReferenceForSame (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForKeywords (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods
41: [ OK ] SelectionCollectionDataTest.HandlesPositionModifiersForMethods (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositions
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositions (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic
41: [ OK ] SelectionCollectionDataTest.HandlesKeywordOfPositionsInArithmetic (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericComparisons
41: [ OK ] SelectionCollectionDataTest.HandlesNumericComparisons (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesArithmeticExpressions
41: [ OK ] SelectionCollectionDataTest.HandlesArithmeticExpressions (8 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericVariables (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesComplexNumericVariables
41: [ OK ] SelectionCollectionDataTest.HandlesComplexNumericVariables (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariables
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariables (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesPositionVariableInModifier
41: [ OK ] SelectionCollectionDataTest.HandlesPositionVariableInModifier (4 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesConstantPositionInVariable
41: [ OK ] SelectionCollectionDataTest.HandlesConstantPositionInVariable (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables
41: [ OK ] SelectionCollectionDataTest.HandlesNumericConstantsInVariables (5 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysis (6 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithVariables (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables
41: [ OK ] SelectionCollectionDataTest.HandlesBooleanStaticAnalysisWithMoreVariables (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesUnusedVariables
41: [ OK ] SelectionCollectionDataTest.HandlesUnusedVariables (2 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithStaticEvaluationGroups (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups (3 ms)
41: [ RUN ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2
41: [ OK ] SelectionCollectionDataTest.HandlesVariablesWithMixedEvaluationGroups2 (4 ms)
41: [----------] 66 tests from SelectionCollectionDataTest (327 ms total)
41:
41: [----------] 17 tests from SelectionOptionTest
41: [ RUN ] SelectionOptionTest.ParsesSimpleSelection
41: [ OK ] SelectionOptionTest.ParsesSimpleSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired
41: [ OK ] SelectionOptionTest.HandlesDynamicSelectionWhenStaticRequired (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired
41: [ OK ] SelectionOptionTest.HandlesNonAtomicSelectionWhenAtomsRequired (3 ms)
41: [ RUN ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired
41: [ OK ] SelectionOptionTest.ChecksForSortedAtomsWhenRequired (2 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptySelections
41: [ OK ] SelectionOptionTest.ChecksEmptySelections (1 ms)
41: [ RUN ] SelectionOptionTest.ChecksEmptyDelayedSelections
41: [ OK ] SelectionOptionTest.ChecksEmptyDelayedSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelections
41: [ OK ] SelectionOptionTest.HandlesTooManySelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDefaultSelectionText
41: [ OK ] SelectionOptionTest.HandlesDefaultSelectionText (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesAdjuster
41: [ OK ] SelectionOptionTest.HandlesAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDynamicWhenStaticRequiredWithAdjuster (2 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooManySelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesTooFewSelectionsWithAdjuster (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedRequiredSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedRequiredSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections
41: [ OK ] SelectionOptionTest.HandlesTooFewDelayedRequiredSelections (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedOptionalSelection
41: [ OK ] SelectionOptionTest.HandlesDelayedOptionalSelection (1 ms)
41: [ RUN ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster
41: [ OK ] SelectionOptionTest.HandlesDelayedSelectionWithAdjuster (1 ms)
41: [----------] 17 tests from SelectionOptionTest (23 ms total)
41:
41: [----------] 9 tests from SelectionFileOptionTest
41: [ RUN ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesSingleSelectionOptionFromFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions
41: [ OK ] SelectionFileOptionTest.HandlesTwoSeparateSelectionOptions (2 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoSelectionOptionsFromSingleFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFile
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFile (2 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet
41: [ OK ] SelectionFileOptionTest.HandlesRequiredOptionFromFileWithOtherOptionSet (1 ms)
41: [ RUN ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile
41: [ OK ] SelectionFileOptionTest.HandlesTwoRequiredOptionsFromSingleFile (2 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNoFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNoFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithNonExistentFile
41: [ OK ] SelectionFileOptionTest.GivesErrorWithNonExistentFile (1 ms)
41: [ RUN ] SelectionFileOptionTest.GivesErrorWithMultipleFiles
41: [ OK ] SelectionFileOptionTest.GivesErrorWithMultipleFiles (2 ms)
41: [----------] 9 tests from SelectionFileOptionTest (13 ms total)
41:
41: [----------] Global test environment tear-down
41: [==========] 192 tests from 11 test cases ran. (1012 ms total)
41: [ PASSED ] 192 tests.
41/54 Test #41: SelectionUnitTests .................. Passed 1.10 sec
test 42
Start 42: MdrunOutputTests
42: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-output-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunOutputTests.xml"
42: Test timeout computed to be: 600
42: [==========] Running 12 tests from 5 test cases.
42: [----------] Global test environment set-up.
42: [----------] 1 test from MdrunTest
42: [ RUN ] MdrunTest.WritesHelp
42: [ OK ] MdrunTest.WritesHelp (50 ms)
42: [----------] 1 test from MdrunTest (50 ms total)
42:
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0
42: Setting the LD random seed to -4325413
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.345 0.173 199.7
42: (ns/day) (hour/ns)
42: Performance: 1.001 23.977
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_0.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/0 (249 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1
42: Setting the LD random seed to -1157661365
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.351 0.176 199.7
42: (ns/day) (hour/ns)
42: Performance: 0.983 24.413
42:
Reading frame 0 time 0.000
42: # Atoms 6
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_1.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/1 (211 ms)
42: [ RUN ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2
42: Setting the LD random seed to -68165638
42: Generated 3 of the 3 non-bonded parameter combinations
42: Generating 1-4 interactions: fudge = 0.5
42: Generated 3 of the 3 1-4 parameter combinations
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group rest is 9.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: NVE simulation: will use the initial temperature of 2573.591 K for
42: determining the Verlet buffer size
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There were 2 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc2'
42: 1 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 2573.59 K
42: Calculated rlist for 1x1 atom pair-list as 1.113 nm, buffer size 0.113 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.104 nm, buffer size 0.104 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.354 0.177 199.7
42: (ns/day) (hour/ns)
42: Performance: 0.975 24.610
42:
Reading frame 0 time 0.000
42: # Atoms 3
42:
Reading frame 1 time 0.001
Last frame 1 time 0.001
42:
42:
42: Item #frames Timestep (ps)
42: Step 2 0.001
42: Time 2 0.001
42: Lambda 0
42: Coords 2 0.001
42: Velocities 0
42: Forces 0
42: Box 2 0.001
42: Checking file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithDifferentOutputGroupSettings_MdrunCompressedXOutput_ExitsNormally_2.xtc
42: [ OK ] WithDifferentOutputGroupSettings/MdrunCompressedXOutput.ExitsNormally/2 (212 ms)
42: [----------] 3 tests from WithDifferentOutputGroupSettings/MdrunCompressedXOutput (672 ms total)
42:
42: [----------] 2 tests from Argon12/OutputFiles
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/0
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.460 0.230 199.8
42: (ns/day) (hour/ns)
42: Performance: 6.376 3.764
42: [ OK ] Argon12/OutputFiles.FilesArePresent/0 (265 ms)
42: [ RUN ] Argon12/OutputFiles.FilesArePresent/1
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
42: that with the Verlet scheme, nstlist has no effect on the accuracy of
42: your simulation.
42:
42:
42: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: Setting nstcalcenergy (100) equal to nstenergy (4)
42:
42: Generated 1 of the 1 non-bonded parameter combinations
42: Excluding 1 bonded neighbours molecule type 'Argon'
42: Number of degrees of freedom in T-Coupling group System is 33.00
42:
42: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1_input.mdp]:
42: NVE simulation: will use the initial temperature of 68.810 K for
42: determining the Verlet buffer size
42:
42:
42: There were 3 notes
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Argon12_OutputFiles_FilesArePresent_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Can not increase nstlist because an NVE ensemble is used
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'Argon'
42: 16 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
42: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
42: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.398 0.199 199.8
42: (ns/day) (hour/ns)
42: Performance: 7.369 3.257
42: [ OK ] Argon12/OutputFiles.FilesArePresent/1 (234 ms)
42: [----------] 2 tests from Argon12/OutputFiles (499 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/Trajectories
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0
42: Setting the LD random seed to -102761515
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.310 0.156 199.6
42: (ns/day) (hour/ns)
42: Performance: 3.889 6.172
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/0 (202 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1
42: Setting the LD random seed to -1572873
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.285 0.143 199.6
42: (ns/day) (hour/ns)
42: Performance: 4.229 5.675
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/1 (189 ms)
42: [ RUN ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2
42: Setting the LD random seed to -1083441693
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_Trajectories_ThatDifferInNstxout_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 6 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.331 0.166 199.6
42: (ns/day) (hour/ns)
42: Performance: 3.653 6.570
42: [ OK ] MdrunCanWrite/Trajectories.ThatDifferInNstxout/2 (211 ms)
42: [----------] 3 tests from MdrunCanWrite/Trajectories (602 ms total)
42:
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0
42: Setting the LD random seed to -1662215229
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.333 0.167 199.7
42: (ns/day) (hour/ns)
42: Performance: 1.556 15.428
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/0 (211 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1
42: Setting the LD random seed to -411043910
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.336 0.168 199.6
42: (ns/day) (hour/ns)
42: Performance: 1.542 15.563
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/1 (213 ms)
42: [ RUN ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2
42: Setting the LD random seed to -146837779
42: Generated 8 of the 10 non-bonded parameter combinations
42: Excluding 2 bonded neighbours molecule type 'Methanol'
42: Excluding 2 bonded neighbours molecule type 'SOL'
42: Number of degrees of freedom in T-Coupling group System is 12.00
42:
42: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2_input.mdp]:
42: You are using a plain Coulomb cut-off, which might produce artifacts.
42: You might want to consider using PME electrostatics.
42:
42:
42:
42: There was 1 note
42: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
42: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunCanWrite_NptTrajectories_WithDifferentPcoupl_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
42: Changing nstlist from 10 to 80, rlist from 1.022 to 1.293
42:
42: Using 1 MPI thread
42: Using 2 OpenMP threads
42:
42:
42: NOTE: The number of threads is not equal to the number of (logical) cores
42: and the -pin option is set to auto: will not pin threads to cores.
42: This can lead to significant performance degradation.
42: Consider using -pin on (and -pinoffset in case you run multiple jobs).
42:
42: WARNING: Using the slow plain C kernels. This should
42: not happen during routine usage on supported platforms.
42: starting mdrun 'spc-and-methanol'
42: 2 steps, 0.0 ps.
42: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
42: Calculated rlist for 1x1 atom pair-list as 1.025 nm, buffer size 0.025 nm
42: Set rlist, assuming 4x4 atom pair-list, to 1.022 nm, buffer size 0.022 nm
42: Note that mdrun will redetermine rlist based on the actual pair-list setup
42: This run will generate roughly 0 Mb of data
42:
42: Writing final coordinates.
42:
42: Core t (s) Wall t (s) (%)
42: Time: 0.330 0.165 199.6
42: (ns/day) (hour/ns)
42: Performance: 1.568 15.309
42: [ OK ] MdrunCanWrite/NptTrajectories.WithDifferentPcoupl/2 (209 ms)
42: [----------] 3 tests from MdrunCanWrite/NptTrajectories (633 ms total)
42:
42: [----------] Global test environment tear-down
42: [==========] 12 tests from 5 test cases ran. (2456 ms total)
42: [ PASSED ] 12 tests.
42/54 Test #42: MdrunOutputTests .................... Passed 2.52 sec
test 43
Start 43: MdrunModulesTests
43: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-modules-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunModulesTests.xml"
43: Test timeout computed to be: 600
43: [==========] Running 10 tests from 3 test cases.
43: [----------] Global test environment set-up.
43: [----------] 4 tests from DensityFittingTest
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct
43: Setting the LD random seed to 2111821784
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -3.85654101644806e+03
43: Maximum force = 2.88468568366558e+03 on atom 3
43: Norm of force = 1.07544474716821e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectInnerProduct.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectInnerProduct (80 ms)
43: [ RUN ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy
43: Setting the LD random seed to -549718290
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = -2.71386626596691e+04
43: Maximum force = 4.34097106676756e+03 on atom 2
43: Norm of force = 1.25497916295893e+03
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_EnergyMinimizationEnergyCorrectForRelativeEntropy.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Last energy frame read 2 time 2.000 This run will generate roughly 0 Mb of data
43: [ OK ] DensityFittingTest.EnergyMinimizationEnergyCorrectForRelativeEntropy (39 ms)
43: [ RUN ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch
43:
43: [WARNING] ./src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 2 threads.
43: [ OK ] DensityFittingTest.GromppErrorWhenEnergyEvaluationFrequencyMismatch (37 ms)
43: [ RUN ] DensityFittingTest.CheckpointWorks
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: Setting nstcalcenergy (100) equal to nstenergy (2)
43:
43: Setting the LD random seed to -310629660
43: Generated 1 of the 1 non-bonded parameter combinations
43: Excluding 1 bonded neighbours molecule type 'Argon'
43: Number of degrees of freedom in T-Coupling group rest is 33.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks_input.mdp]:
43: NVE simulation: will use the initial temperature of 68.810 K for
43: determining the Verlet buffer size
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 68.8096 K
43: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.341 0.171 199.7
43: (ns/day) (hour/ns)
43: Performance: 1.520 15.790
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Overriding nsteps with value passed on the command line: 4 steps, 0.004 ps
43: Can not increase nstlist because an NVE ensemble is used
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting mdrun 'Argon'
43: 6 steps, 0.0 ps (continuing from step 2, 0.0 ps).
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.378 0.189 199.8
43: (ns/day) (hour/ns)
43: Performance: 2.284 10.509
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DensityFittingTest_CheckpointWorks.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.002
Last energy frame read 1 time 0.002 [ OK ] DensityFittingTest.CheckpointWorks (407 ms)
43: [----------] 4 tests from DensityFittingTest (563 ms total)
43:
43: [----------] 4 tests from MimicTest
43: [ RUN ] MimicTest.OneQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -191385603
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.001 184.3
43: (ns/day) (hour/ns)
43: Performance: 61.432 0.391
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.OneQuantumMol (35 ms)
43: [ RUN ] MimicTest.AllQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -1087520769
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.001 184.0
43: (ns/day) (hour/ns)
43: Performance: 61.536 0.390
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.AllQuantumMol (35 ms)
43: [ RUN ] MimicTest.TwoQuantumMol
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -538492935
43: Generated 10 of the 10 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 10 of the 10 1-4 parameter combinations
43: Excluding 2 bonded neighbours molecule type 'SOL'
43: Number of degrees of freedom in T-Coupling group rest is 21.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: NVE simulation with an initial temperature of zero: will use a Verlet
43: buffer of 10%. Check your energy drift!
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
43:
43: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.003 0.001 183.7
43: (ns/day) (hour/ns)
43: Performance: 62.384 0.385
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.TwoQuantumMol (35 ms)
43: [ RUN ] MimicTest.BondCuts
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: For a correct single-point energy evaluation with nsteps = 0, use
43: continuation = yes to avoid constraining the input coordinates.
43:
43: Setting the LD random seed to -8526217
43: Generated 2211 of the 2211 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 0.5
43: Generated 2211 of the 2211 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
43: Number of degrees of freedom in T-Coupling group rest is 66.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: NVE simulation: will use the initial temperature of 300.368 K for
43: determining the Verlet buffer size
43:
43:
43: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 3 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Can not increase nstlist because an NVE ensemble is used
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
43:
43: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
43:
Reading frame 0 time 0.000
Last frame 0 time 0.000
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.006 0.003 191.6
43: (ns/day) (hour/ns)
43: Performance: 27.829 0.862
43: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
43:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
43: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43: [ OK ] MimicTest.BondCuts (138 ms)
43: [----------] 4 tests from MimicTest (243 ms total)
43:
43: [----------] 2 tests from WithIntegrator/ImdTest
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/0
43: Setting the LD random seed to 804883311
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43:
43: NOTE 1 [file glycine_vacuo.top, line 12]:
43: The bond in molecule-type Glycine between atoms 1 N and 2 H1 has an
43: estimated oscillational period of 1.0e-02 ps, which is less than 10 times
43: the time step of 2.0e-03 ps.
43: Maybe you forgot to change the constraints mdp option.
43:
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Changing nstlist from 10 to 50, rlist from 1.026 to 1.34
43:
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 43805.
43: IMD: -imdwait not set, starting simulation.
43: starting mdrun 'Glycine'
43: 2 steps, 0.0 ps.
43: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
43: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
43: Set rlist, assuming 4x4 atom pair-list, to 1.026 nm, buffer size 0.026 nm
43: Note that mdrun will redetermine rlist based on the actual pair-list setup
43: This run will generate roughly 0 Mb of data
43:
43: Writing final coordinates.
43:
43: Core t (s) Wall t (s) (%)
43: Time: 0.446 0.223 199.7
43: (ns/day) (hour/ns)
43: Performance: 2.322 10.336
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/0 (1345 ms)
43: [ RUN ] WithIntegrator/ImdTest.ImdCanRun/1
43:
43: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: Setting tcoupl from 'V-rescale' to 'no'. Temperature coupling does not
43: apply to steep.
43:
43: Setting the LD random seed to 1902695679
43: Generated 20503 of the 20503 non-bonded parameter combinations
43: Generating 1-4 interactions: fudge = 1
43: Generated 17396 of the 20503 1-4 parameter combinations
43: Excluding 3 bonded neighbours molecule type 'Glycine'
43: Group 'Heavy_Atoms' with 5 atoms can be activated for interactive molecular dynamics (IMD).
43: Number of degrees of freedom in T-Coupling group System is 27.00
43:
43: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1_input.mdp]:
43: You are using a plain Coulomb cut-off, which might produce artifacts.
43: You might want to consider using PME electrostatics.
43:
43:
43:
43: There were 2 notes
43: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
43: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/WithIntegrator_ImdTest_ImdCanRun_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
43: Using 1 MPI thread
43: Using 2 OpenMP threads
43:
43:
43: NOTE: The number of threads is not equal to the number of (logical) cores
43: and the -pin option is set to auto: will not pin threads to cores.
43: This can lead to significant performance degradation.
43: Consider using -pin on (and -pinoffset in case you run multiple jobs).
43:
43: WARNING: Using the slow plain C kernels. This should
43: not happen during routine usage on supported platforms.
43:
43: IMD: Enabled. This simulation will accept incoming IMD connections.
43: IMD: Pulling from IMD remote is enabled (-imdpull).
43: IMD: Setting port for connection requests to 0.
43: IMD: Setting up incoming socket.
43: IMD: Listening for IMD connection on port 56813.
43: IMD: -imdwait not set, starting simulation.
43:
43: Steepest Descents:
43: Tolerance (Fmax) = 1.00000e+01
43: Number of steps = 2
43:
43: Energy minimization reached the maximum number of steps before the forces
43: reached the requested precision Fmax < 10.
43:
43: writing lowest energy coordinates.
43:
43: Steepest Descents did not converge to Fmax < 10 in 3 steps.
43: Potential Energy = 1.19770464690297e+03
43: Maximum force = 1.77948604657896e+04 on atom 9
43: Norm of force = 7.87328617833980e+03
43: This run will generate roughly 0 Mb of data
43: [ OK ] WithIntegrator/ImdTest.ImdCanRun/1 (1116 ms)
43: [----------] 2 tests from WithIntegrator/ImdTest (2461 ms total)
43:
43: [----------] Global test environment tear-down
43: [==========] 10 tests from 3 test cases ran. (3269 ms total)
43: [ PASSED ] 10 tests.
43/54 Test #43: MdrunModulesTests ................... Passed 3.34 sec
test 44
Start 44: MdrunIOTests
44: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-io-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunIOTests.xml"
44: Test timeout computed to be: 600
44: [==========] Running 51 tests from 9 test cases.
44: [----------] Global test environment set-up.
44: [----------] 3 tests from GromppTest
44: [ RUN ] GromppTest.EmptyMdpFileWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -1141117783
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_EmptyMdpFileWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.EmptyMdpFileWorks (28 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorks
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -671748185
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group rest: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group rest is 12.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorks_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorks (24 ms)
44: [ RUN ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: For a correct single-point energy evaluation with nsteps = 0, use
44: continuation = yes to avoid constraining the input coordinates.
44:
44: Setting the LD random seed to -539263506
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Simulated annealing for group Methanol: Single, 3 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 3.0 280.0
44: 6.0- 270.0
44: Simulated annealing for group SOL: Periodic, 4 timepoints
44: Time (ps) Temperature (K)
44: 0.0 298.0
44: 2.0 320.0
44: 4.0 320.0
44: 6.0 298.0
44: Number of degrees of freedom in T-Coupling group Methanol is 7.20
44: Number of degrees of freedom in T-Coupling group SOL is 4.80
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: NVE simulation: will use the initial temperature of 1046.791 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/GromppTest_SimulatedAnnealingWorksWithMultipleGroups_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
44: Calculated rlist for 1x1 atom pair-list as 1.061 nm, buffer size 0.061 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.056 nm, buffer size 0.056 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: [ OK ] GromppTest.SimulatedAnnealingWorksWithMultipleGroups (23 ms)
44: [----------] 3 tests from GromppTest (75 ms total)
44:
44: [----------] 6 tests from MdrunTerminationTest
44: [ RUN ] MdrunTerminationTest.CheckpointRestartAppendsByDefault
44: Setting the LD random seed to -1097876865
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.353 0.177 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.468 16.352
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartAppendsByDefault.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.391 0.196 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.323 18.137
44: [ OK ] MdrunTerminationTest.CheckpointRestartAppendsByDefault (474 ms)
44: [ RUN ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
44: Setting the LD random seed to -135269187
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 1, rlist from 1.024 to 1
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 100 steps, 0.1 ps.
44:
44: Step 1: Run time exceeded 0.000 hours, will terminate the run within 2 steps
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.276 0.138 199.6
44: (ns/day) (hour/ns)
44: Performance: 1.875 12.798
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Setting nsteps to 102
44: Writing statusfile with starting step 0 and length 102 steps...
44: time 0.000 and length 0.102 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_WritesCheckpointAfterMaxhTerminationAndThenRestarts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 102 steps, 0.1 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.275 0.138 199.7
44: (ns/day) (hour/ns)
44: Performance: 63.435 0.378
44: [ OK ] MdrunTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (333 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend
44: Setting the LD random seed to -271335443
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.284 0.142 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.823 13.163
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.290 0.145 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.786 13.436
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Setting nsteps to 6
44: Writing statusfile with starting step 0 and length 6 steps...
44: time 0.000 and length 0.006 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 6 steps, 0.0 ps (continuing from step 4, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.254 0.127 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.036 11.789
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Setting nsteps to 8
44: Writing statusfile with starting step 0 and length 8 steps...
44: time 0.000 and length 0.008 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 6, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.297 0.149 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.744 13.763
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWithNoAppendWorksAndCannotLaterAppend.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.002 0.001 180.8
44: (ns/day) (hour/ns)
44: Performance: 71.196 0.337
44: [ OK ] MdrunTerminationTest.CheckpointRestartWithNoAppendWorksAndCannotLaterAppend (686 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile
44: Setting the LD random seed to 2147218778
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.273 0.137 199.6
44: (ns/day) (hour/ns)
44: Performance: 1.897 12.649
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.277 0.139 199.4
44: (ns/day) (hour/ns)
44: Performance: 3.112 7.713
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithMissingCheckpointFile (347 ms)
44: [ RUN ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile
44: Setting the LD random seed to -539069491
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.254 0.127 199.6
44: (ns/day) (hour/ns)
44: Performance: 2.037 11.782
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: [ OK ] MdrunTerminationTest.CheckpointRestartWorksEvenWithAppendAndMissingCheckpointFile (170 ms)
44: [ RUN ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles
44: Setting the LD random seed to -135174865
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There was 1 note
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 2 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 1.026 nm, buffer size 0.026 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.024 nm, buffer size 0.024 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.268 0.134 199.6
44: (ns/day) (hour/ns)
44: Performance: 1.929 12.439
44: Reading toplogy and stuff from /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Setting nsteps to 4
44: Writing statusfile with starting step 0 and length 4 steps...
44: time 0.000 and length 0.004 ps
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunTerminationTest_RunWithNoAppendCreatesPartFiles.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 10 to 80, rlist from 1.024 to 1.244
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.300 0.150 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.724 13.921
44: [ OK ] MdrunTerminationTest.RunWithNoAppendCreatesPartFiles (340 ms)
44: [----------] 6 tests from MdrunTerminationTest (2353 ms total)
44:
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.475 0.238 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.177 3.885
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.420 0.210 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.697 6.492
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.464 0.232 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.347 7.170
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (771 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.555 0.278 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.287 4.540
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.376 0.188 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.133 5.806
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.424 0.212 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.667 6.545
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (765 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.409 0.205 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.181 3.342
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.384 0.192 199.6
44: (ns/day) (hour/ns)
44: Performance: 4.044 5.935
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.419 0.210 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.708 6.472
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (689 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.407 0.204 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.203 3.332
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.401 0.201 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.868 6.205
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.377 0.189 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.118 5.829
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (677 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.450 0.225 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.526 3.677
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.423 0.212 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.665 6.549
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.400 0.200 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.878 6.188
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (722 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: NVE simulation: will use the initial temperature of 2573.591 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 2573.59 K
44: Calculated rlist for 1x1 atom pair-list as 0.880 nm, buffer size 0.180 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.880 nm, buffer size 0.180 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.428 0.214 199.9
44: (ns/day) (hour/ns)
44: Performance: 6.852 3.503
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.425 0.213 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.654 6.567
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.379 0.190 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.103 5.849
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (706 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.731 nm, buffer size 0.031 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.731 nm, buffer size 0.031 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.433 0.217 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.779 3.540
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.375 0.188 199.4
44: (ns/day) (hour/ns)
44: Performance: 4.141 5.796
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.731 to 0.816
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.346 0.173 199.6
44: (ns/day) (hour/ns)
44: Performance: 4.490 5.345
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (683 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 3 of the 3 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 3 of the 3 1-4 parameter combinations
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 9.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.754 nm, buffer size 0.054 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.754 nm, buffer size 0.054 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.369 0.185 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.942 3.022
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.350 0.176 199.4
44: (ns/day) (hour/ns)
44: Performance: 4.428 5.420
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.754 to 1.017
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc2'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.328 0.164 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.734 5.070
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_7_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (622 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.437 0.219 199.7
44: (ns/day) (hour/ns)
44: Performance: 6.709 3.577
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.434 0.218 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.575 6.714
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.478 0.240 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.246 7.393
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (1001 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: NVE simulation: will use the initial temperature of 456.887 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 6 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
44: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.521 0.261 199.7
44: (ns/day) (hour/ns)
44: Performance: 5.635 4.259
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.501 0.251 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.098 7.748
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.447 0.224 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.473 6.911
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (1066 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.572 0.286 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.134 4.675
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.330 0.665 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.169 20.536
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.596 0.298 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.606 9.211
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_10_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (1800 ms)
44: [ RUN ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2145 of the 2145 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2145 of the 2145 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
44:
44: NOTE 3 [file unknown]:
44: You are using constraints on all bonds, whereas the forcefield has been
44: parametrized only with constraints involving hydrogen atoms. We suggest
44: using constraints = h-bonds instead, this will also improve performance.
44:
44: Cleaning up constraints and constant bonded interactions with virtual sites
44: Removed 18 Angles with virtual sites, 21 left
44: Removed 10 Proper Dih.s with virtual sites, 44 left
44: Converted 15 Constraints with virtual sites to connections, 7 left
44: Number of degrees of freedom in T-Coupling group System is 23.00
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: There are 9 non-linear virtual site constructions. Their contribution to
44: the energy error is approximated. In most cases this does not affect the
44: error significantly.
44:
44:
44: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 5 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps.
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning all bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.847 0.424 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.466 6.925
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.378 0.189 199.5
44: (ns/day) (hour/ns)
44: Performance: 4.105 5.846
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Alanine dipeptide in vacuo'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.401 0.201 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.876 6.192
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegrators_MdrunNoAppendContinuationIsExact_WithinTolerances_11_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegrators/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (1289 ms)
44: [----------] 12 tests from NormalIntegrators/MdrunNoAppendContinuationIsExact (10795 ms total)
44:
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.613 0.307 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.784 5.017
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 3.115 1.558 199.9
44: (ns/day) (hour/ns)
44: Performance: 0.499 48.092
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.704 0.353 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.206 10.881
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (2544 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 293.480 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 4 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
44: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.530 0.265 199.9
44: (ns/day) (hour/ns)
44: Performance: 5.536 4.335
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.476 0.238 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.263 7.355
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.475 0.238 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.269 7.342
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1056 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.728 nm, buffer size 0.028 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.590 0.295 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.973 4.826
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.478 0.240 199.4
44: (ns/day) (hour/ns)
44: Performance: 3.242 7.402
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.728 to 0.805
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.592 0.296 199.7
44: (ns/day) (hour/ns)
44: Performance: 2.623 9.150
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1410 ms)
44: [ RUN ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 2485 of the 2485 non-bonded parameter combinations
44: Generating 1-4 interactions: fudge = 0.5
44: Generated 2485 of the 2485 1-4 parameter combinations
44: Excluding 3 bonded neighbours molecule type 'nonanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group System is 79.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
44: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.643 0.322 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.564 5.259
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.594 0.298 199.5
44: (ns/day) (hour/ns)
44: Performance: 2.612 9.187
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun '30 system in water'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.581 0.291 199.7
44: (ns/day) (hour/ns)
44: Performance: 2.672 8.983
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalIntegratorsWithFEP_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1396 ms)
44: [----------] 4 tests from NormalIntegratorsWithFEP/MdrunNoAppendContinuationIsExact (6409 ms total)
44:
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.424 0.212 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.917 3.470
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.335 0.668 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.165 20.608
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.535 0.268 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.906 8.259
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (1231 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.408 0.204 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.188 3.339
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.379 0.190 199.6
44: (ns/day) (hour/ns)
44: Performance: 4.097 5.858
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.401 0.201 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.875 6.194
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (689 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.408 0.204 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.192 3.337
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.403 0.202 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.851 6.232
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.415 0.208 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.744 6.410
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (723 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.472 0.236 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.222 3.857
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.468 0.234 199.5
44: (ns/day) (hour/ns)
44: Performance: 3.318 7.234
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.462 0.231 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.364 7.134
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (790 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.420 0.210 199.9
44: (ns/day) (hour/ns)
44: Performance: 6.984 3.437
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.425 0.213 199.9
44: (ns/day) (hour/ns)
44: Performance: 3.657 6.563
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.388 0.194 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.006 5.991
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (710 ms)
44: [ RUN ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.406 0.203 199.8
44: (ns/day) (hour/ns)
44: Performance: 7.218 3.325
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.513 0.257 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.029 7.925
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.356 0.178 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.358 5.508
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NVT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NVT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (721 ms)
44: [----------] 6 tests from NVT/MdrunNoAppendContinuationIsExact (4864 ms total)
44:
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.409 0.205 199.7
44: (ns/day) (hour/ns)
44: Performance: 7.178 3.344
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.394 0.197 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.942 6.089
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.455 0.228 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.418 7.022
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (719 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.459 0.230 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.390 3.756
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.424 0.213 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.658 6.561
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.357 0.179 199.7
44: (ns/day) (hour/ns)
44: Performance: 4.351 5.516
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (703 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.719 0.360 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.080 5.882
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.691 0.346 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.248 10.678
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.508 0.754 199.9
44: (ns/day) (hour/ns)
44: Performance: 1.031 23.285
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (1547 ms)
44: [ RUN ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: NVE simulation: will use the initial temperature of 68.810 K for
44: determining the Verlet buffer size
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.625 0.312 199.9
44: (ns/day) (hour/ns)
44: Performance: 4.701 5.105
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.381 0.691 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.125 21.326
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.421 0.211 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.689 6.506
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPH_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPH/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (1297 ms)
44: [----------] 4 tests from NPH/MdrunNoAppendContinuationIsExact (4267 ms total)
44:
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.427 0.214 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.871 3.493
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.495 0.248 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.137 7.650
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.458 0.229 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.392 7.076
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (789 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.478 0.240 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.133 3.913
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 1.424 0.712 199.8
44: (ns/day) (hour/ns)
44: Performance: 1.091 21.989
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.488 0.244 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.185 7.536
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_1_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/1 (1288 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.628 0.314 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.674 5.135
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.557 0.279 199.6
44: (ns/day) (hour/ns)
44: Performance: 2.787 8.612
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.442 0.221 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.514 6.830
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_2_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/2 (900 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.431 0.216 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.811 3.524
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.369 0.185 199.4
44: (ns/day) (hour/ns)
44: Performance: 4.197 5.719
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.395 0.198 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.937 6.096
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_3_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/3 (705 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44:
44: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_input.mdp]:
44: Using Berendsen pressure coupling invalidates the true ensemble for the
44: thermostat
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: There was 1 warning
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.438 0.219 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.695 3.585
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.546 0.273 199.7
44: (ns/day) (hour/ns)
44: Performance: 2.845 8.436
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.448 0.224 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.470 6.916
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_4_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/4 (814 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_input.mdp]:
44: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.518 0.259 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.666 4.236
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.468 0.234 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.319 7.231
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.467 0.234 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.328 7.212
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_5_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/5 (811 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_input.mdp]:
44: The Berendsen thermostat does not generate the correct kinetic energy
44: distribution. You might want to consider using the V-rescale thermostat.
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.614 0.307 199.8
44: (ns/day) (hour/ns)
44: Performance: 4.783 5.018
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.464 0.233 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.343 7.178
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.645 0.323 199.8
44: (ns/day) (hour/ns)
44: Performance: 2.410 9.960
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_6_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/6 (967 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/7 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.562 0.281 199.8
44: (ns/day) (hour/ns)
44: Performance: 5.226 4.592
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.379 0.190 199.6
44: (ns/day) (hour/ns)
44: Performance: 4.098 5.857
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.400 0.200 199.7
44: (ns/day) (hour/ns)
44: Performance: 3.879 6.188
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_8_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/8 (756 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.560 0.280 199.9
44: (ns/day) (hour/ns)
44: Performance: 5.246 4.575
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.447 0.224 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.476 6.904
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.556 0.278 199.9
44: (ns/day) (hour/ns)
44: Performance: 2.797 8.580
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NPT_MdrunNoAppendContinuationIsExact_WithinTolerances_9_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/9 (887 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/10 (0 ms)
44: [ RUN ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11
44: [ OK ] NPT/MdrunNoAppendContinuationIsExact.WithinTolerances/11 (0 ms)
44: [----------] 12 tests from NPT/MdrunNoAppendContinuationIsExact (7922 ms total)
44:
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact
44: [ RUN ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
44: that with the Verlet scheme, nstlist has no effect on the accuracy of
44: your simulation.
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_input.mdp]:
44: Setting nstcalcenergy (100) equal to nstenergy (4)
44:
44: Generated 1 of the 1 non-bonded parameter combinations
44: Excluding 1 bonded neighbours molecule type 'Argon'
44: Number of degrees of freedom in T-Coupling group System is 33.00
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps.
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
44: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
44: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.450 0.225 199.8
44: (ns/day) (hour/ns)
44: Performance: 6.520 3.681
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 8 steps, 0.0 ps.
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.468 0.234 199.6
44: (ns/day) (hour/ns)
44: Performance: 3.316 7.237
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
44:
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'Argon'
44: 16 steps, 0.0 ps (continuing from step 8, 0.0 ps).
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.467 0.234 199.8
44: (ns/day) (hour/ns)
44: Performance: 3.325 7.218
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_full.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_firstpart.edr as double precision energy file
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MTTK_MdrunNoAppendContinuationIsExact_WithinTolerances_0_secondpart.part0002.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Last energy frame read 2 time 0.008
Reading energy frame 0 time 0.008
Reading energy frame 1 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 2 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 2 time 0.016 [ OK ] MTTK/MdrunNoAppendContinuationIsExact.WithinTolerances/0 (776 ms)
44: [----------] 1 test from MTTK/MdrunNoAppendContinuationIsExact (776 ms total)
44:
44: [----------] 3 tests from Checking/InitialConstraintsTest
44: [ RUN ] Checking/InitialConstraintsTest.Works/0
44: Setting the LD random seed to -1688227955
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.266 0.133 199.6
44: (ns/day) (hour/ns)
44: Performance: 1.297 18.500
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_0_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/0 (174 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/1
44: Setting the LD random seed to -71311661
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 2 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.297 0.149 199.7
44: (ns/day) (hour/ns)
44: Performance: 1.162 20.657
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_1_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/1 (189 ms)
44: [ RUN ] Checking/InitialConstraintsTest.Works/2
44:
44: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: Integrator method md-vv-avek is implemented primarily for validation
44: purposes; for molecular dynamics, you should probably be using md or md-vv
44:
44: Setting the LD random seed to 1001912316
44: Generated 8 of the 10 non-bonded parameter combinations
44: Excluding 2 bonded neighbours molecule type 'Methanol'
44: Excluding 2 bonded neighbours molecule type 'SOL'
44: Number of degrees of freedom in T-Coupling group rest is 11.00
44:
44: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: NVE simulation: will use the initial temperature of 1141.954 K for
44: determining the Verlet buffer size
44:
44:
44: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_input.mdp]:
44: You are using a plain Coulomb cut-off, which might produce artifacts.
44: You might want to consider using PME electrostatics.
44:
44:
44:
44: There were 3 notes
44: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
44: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
44: Can not increase nstlist because an NVE ensemble is used
44: Using 1 MPI thread
44:
44: Non-default thread affinity set, disabling internal thread affinity
44:
44: Using 2 OpenMP threads
44:
44:
44: WARNING: Using the slow plain C kernels. This should
44: not happen during routine usage on supported platforms.
44: starting mdrun 'spc-and-methanol'
44: 1 steps, 0.0 ps.
44: turning H bonds into constraints...
44: turning H bonds into constraints...
44: Determining Verlet buffer for a tolerance of 0.0001 kJ/mol/ps at 1141.95 K
44: Calculated rlist for 1x1 atom pair-list as 1.101 nm, buffer size 0.101 nm
44: Set rlist, assuming 4x4 atom pair-list, to 1.096 nm, buffer size 0.096 nm
44: Note that mdrun will redetermine rlist based on the actual pair-list setup
44: This run will generate roughly 0 Mb of data
44:
44: Writing final coordinates.
44:
44: Core t (s) Wall t (s) (%)
44: Time: 0.273 0.137 199.6
44: (ns/day) (hour/ns)
44: Performance: 1.263 19.007
44: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Checking_InitialConstraintsTest_Works_2_spc-and-methanol.edr as double precision energy file
44:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001 [ OK ] Checking/InitialConstraintsTest.Works/2 (178 ms)
44: [----------] 3 tests from Checking/InitialConstraintsTest (541 ms total)
44:
44: [----------] Global test environment tear-down
44: [==========] 51 tests from 9 test cases ran. (38004 ms total)
44: [ PASSED ] 51 tests.
44/54 Test #44: MdrunIOTests ........................ Passed 38.11 sec
test 45
Start 45: MdrunTests
45: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTests.xml"
45: Test timeout computed to be: 600
45: [==========] Running 24 tests from 7 test cases.
45: [----------] Global test environment set-up.
45: [----------] 1 test from DispersionCorrectionTest
45: [ RUN ] DispersionCorrectionTest.DispersionCorrectionCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to -138903561
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
45: Cleaning up constraints and constant bonded interactions with virtual sites
45: Converted 3 Bonds with virtual sites to connections, 7 left
45: Removed 18 Angles with virtual sites, 21 left
45: Removed 10 Proper Dih.s with virtual sites, 44 left
45: Converted 12 Constraints with virtual sites to connections, 0 left
45: Number of degrees of freedom in T-Coupling group System is 30.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: There are 9 non-linear virtual site constructions. Their contribution to
45: the energy error is approximated. In most cases this does not affect the
45: error significantly.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DispersionCorrectionTest_DispersionCorrectionCanRun.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 10 to 50, rlist from 1.016 to 1.167
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Alanine dipeptide in vacuo'
45: 200 steps, 0.4 ps.
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.028 nm, buffer size 0.028 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.016 nm, buffer size 0.016 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.599 0.300 199.7
45: (ns/day) (hour/ns)
45: Performance: 115.802 0.207
45: [ OK ] DispersionCorrectionTest.DispersionCorrectionCanRun (532 ms)
45: [----------] 1 test from DispersionCorrectionTest (532 ms total)
45:
45: [----------] 1 test from OriresTest
45: [ RUN ] OriresTest.OriresCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to 1532742645
45: Generated 2145 of the 2145 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 2145 of the 2145 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 518.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/OriresTest_OriresCanRun.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Orientation restraints only supports a single rank. Choosing to use only a single thread-MPI rank.
45: Changing nstlist from 10 to 25, rlist from 1.054 to 1.164
45:
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'GUANINE NUCLEOTIDE-BINDING PROTEIN G(T), ALPHA-1'
45: 10 steps, 0.0 ps.
45: turning H bonds into constraints...
45: turning H bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.073 nm, buffer size 0.073 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.054 nm, buffer size 0.054 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.543 0.272 199.7
45: (ns/day) (hour/ns)
45: Performance: 6.987 3.435
45: [ OK ] OriresTest.OriresCanRun (2355 ms)
45: [----------] 1 test from OriresTest (2356 ms total)
45:
45: [----------] 3 tests from PmeTest
45: [ RUN ] PmeTest.ReproducesEnergies
45: Setting the LD random seed to 2003299071
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.891 0.446 199.9
45: (ns/day) (hour/ns)
45: Performance: 4.072 5.893
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.748 0.374 199.9
45: (ns/day) (hour/ns)
45: Performance: 4.849 4.949
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45:
45: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
45: starting mdrun 'spc-and-methanol'
45: 20 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.813 0.407 199.9
45: (ns/day) (hour/ns)
45: Performance: 4.463 5.378
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (1452 ms)
45: [ RUN ] PmeTest.ScalesTheBox
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -818677901
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group rest is 12.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: NVE simulation: will use the initial temperature of 1046.791 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.027 0.014 195.3
45: (ns/day) (hour/ns)
45: Performance: 6.273 3.826
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBox (94 ms)
45: [ RUN ] PmeTest.ScalesTheBoxWithWalls
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -8913921
45: Generated 8 of the 10 non-bonded parameter combinations
45: Excluding 2 bonded neighbours molecule type 'Methanol'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Searching the wall atom type(s)
45: Number of degrees of freedom in T-Coupling group rest is 13.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: NVE simulation: will use the initial temperature of 966.268 K for
45: determining the Verlet buffer size
45:
45: Estimate for the relative computational load of the PME mesh part: 1.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
45: The optimal PME mesh load for parallel simulations is below 0.5
45: and for highly parallel simulations between 0.25 and 0.33,
45: for higher performance, increase the cut-off and the PME grid spacing.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc-and-methanol'
45: 0 steps, 0.0 ps.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.098 0.049 198.4
45: (ns/day) (hour/ns)
45: Performance: 1.749 13.718
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
45: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: Calculating fourier grid dimensions for X Y Z
45: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
45: This run will generate roughly 0 Mb of data
45: [ OK ] PmeTest.ScalesTheBoxWithWalls (255 ms)
45: [----------] 3 tests from PmeTest (1802 ms total)
45:
45: [----------] 1 test from CompelTest
45: [ RUN ] CompelTest.SwapCanRun
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: The Berendsen thermostat does not generate the correct kinetic energy
45: distribution. You might want to consider using the V-rescale thermostat.
45:
45: Setting the LD random seed to -1447040655
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 1 bonded neighbours molecule type 'NA'
45: Excluding 1 bonded neighbours molecule type 'CL'
45: Excluding 3 bonded neighbours molecule type 'Protein'
45: Excluding 3 bonded neighbours molecule type 'OCT'
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Split0 group 'Ch0' contains 83 atoms.
45: Split1 group 'Ch1' contains 83 atoms.
45: Solvent group 'SOL' contains 11931 atoms.
45: Swap group 'NA+' contains 19 atoms.
45: Swap group 'CL-' contains 19 atoms.
45: Number of degrees of freedom in T-Coupling group System is 27869.00
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: Removing center of mass motion in the presence of position restraints
45: might cause artifacts. When you are using position restraints to
45: equilibrate a macro-molecule, the artifacts are usually negligible.
45:
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Determining initial numbers of ions per compartment.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 2 steps, 0.0 ps.
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: turning all bonds into constraints...
45: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K
45: Calculated rlist for 1x1 atom pair-list as 1.314 nm, buffer size 0.314 nm
45: Set rlist, assuming 4x4 atom pair-list, to 1.260 nm, buffer size 0.260 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 1 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 7.298 3.649 200.0
45: (ns/day) (hour/ns)
45: Performance: 0.355 67.580
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/CompelTest_SwapCanRun.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Overriding nsteps with value passed on the command line: 2 steps, 0.01 ps
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: SWAP: Setting pointers for checkpoint writing
45: SWAP: Copying channel fluxes from checkpoint file data
45: SWAP: Channel 0 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 1 flux history for ion type NA+ (charge 1): 0 molecules
45: SWAP: Channel 0 flux history for ion type CL- (charge -1): 0 molecules
45: SWAP: Channel 1 flux history for ion type CL- (charge -1): 0 molecules
45: starting mdrun 'Channel_coco in octane membrane'
45: 4 steps, 0.0 ps (continuing from step 2, 0.0 ps).
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 6.290 3.145 200.0
45: (ns/day) (hour/ns)
45: Performance: 0.412 58.248
45: [ OK ] CompelTest.SwapCanRun (12870 ms)
45: [----------] 1 test from CompelTest (12870 ms total)
45:
45: [----------] 6 tests from BondedInteractionsTest
45: [ RUN ] BondedInteractionsTest.NormalBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 2145582875
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalBondWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 186.4
45: (ns/day) (hour/ns)
45: Performance: 48.441 0.495
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalBondWorks (38 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedBondWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 1811912774
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedBondWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 2 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedBondWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.004 0.002 187.8
45: (ns/day) (hour/ns)
45: Performance: 44.323 0.541
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedBondWorks (46 ms)
45: [ RUN ] BondedInteractionsTest.NormalAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to 2013265597
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalAngleWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 186.6
45: (ns/day) (hour/ns)
45: Performance: 49.710 0.483
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalAngleWorks (37 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedAngleWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -167792665
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedAngleWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedAngleWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 187.1
45: (ns/day) (hour/ns)
45: Performance: 46.490 0.516
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedAngleWorks (41 ms)
45: [ RUN ] BondedInteractionsTest.NormalDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -285554506
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_NormalDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_NormalDihedralWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 186.3
45: (ns/day) (hour/ns)
45: Performance: 51.177 0.469
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.NormalDihedralWorks (38 ms)
45: [ RUN ] BondedInteractionsTest.TabulatedDihedralWorks
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: For a correct single-point energy evaluation with nsteps = 0, use
45: continuation = yes to avoid constraining the input coordinates.
45:
45: Setting the LD random seed to -1107461125
45: Generated 3 of the 3 non-bonded parameter combinations
45: Excluding 3 bonded neighbours molecule type 'butane'
45:
45: NOTE 2 [file BondedInteractionsTest_TabulatedDihedralWorks_butane1.top, line 31]:
45: In moleculetype 'butane' 4 atoms are not bound by a potential or
45: constraint to any other atom in the same moleculetype. Although
45: technically this might not cause issues in a simulation, this often means
45: that the user forgot to add a bond/potential/constraint or put multiple
45: molecules in the same moleculetype definition by mistake. Run with -v to
45: get information for each atom.
45:
45: Number of degrees of freedom in T-Coupling group rest is 9.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks_input.mdp]:
45: NVE simulation with an initial temperature of zero: will use a Verlet
45: buffer of 10%. Check your energy drift!
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BondedInteractionsTest_TabulatedDihedralWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting md rerun 'A single butane', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/butane1.gro'
45:
45: Reading frames from gro file 'A single butane', 4 atoms.
45:
Reading frame 0 time 0.000
Last frame 0 time 0.000
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.003 0.002 186.1
45: (ns/day) (hour/ns)
45: Performance: 47.815 0.502
45: This run will generate roughly 0 Mb of data
45: [ OK ] BondedInteractionsTest.TabulatedDihedralWorks (46 ms)
45: [----------] 6 tests from BondedInteractionsTest (246 ms total)
45:
45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.423 0.212 199.8
45: (ns/day) (hour/ns)
45: Performance: 6.943 3.457
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.447 0.224 199.8
45: (ns/day) (hour/ns)
45: Performance: 6.558 3.660
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016 trr version: GMX_trn_file (double precision)
45:
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/0 (492 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.438 0.219 199.9
45: (ns/day) (hour/ns)
45: Performance: 6.704 3.580
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.380 0.190 199.7
45: (ns/day) (hour/ns)
45: Performance: 7.711 3.113
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/1 (467 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.497 0.249 199.9
45: (ns/day) (hour/ns)
45: Performance: 5.911 4.061
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.466 0.233 199.8
45: (ns/day) (hour/ns)
45: Performance: 6.292 3.814
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/2 (4915 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.528 0.264 199.9
45: (ns/day) (hour/ns)
45: Performance: 5.560 4.316
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.508 0.254 199.8
45: (ns/day) (hour/ns)
45: Performance: 5.772 4.158
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultModular_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest.WithinTolerances/3 (4965 ms)
45: [----------] 4 tests from SimulatorsAreEquivalentDefaultModular/SimulatorComparisonTest (10840 ms total)
45:
45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.423 0.212 199.8
45: (ns/day) (hour/ns)
45: Performance: 6.943 3.457
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.409 0.205 199.9
45: (ns/day) (hour/ns)
45: Performance: 7.173 3.346
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_0_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/0 (487 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_input.mdp]:
45: NVE simulation: will use the initial temperature of 68.810 K for
45: determining the Verlet buffer size
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.496 0.248 199.8
45: (ns/day) (hour/ns)
45: Performance: 5.915 4.057
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.464 0.232 199.9
45: (ns/day) (hour/ns)
45: Performance: 6.330 3.792
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_1_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/1 (548 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.367 0.184 199.7
45: (ns/day) (hour/ns)
45: Performance: 7.995 3.002
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.393 0.197 199.8
45: (ns/day) (hour/ns)
45: Performance: 7.460 3.217
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_2_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/2 (456 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 1 of the 1 non-bonded parameter combinations
45: Excluding 1 bonded neighbours molecule type 'Argon'
45: Number of degrees of freedom in T-Coupling group System is 33.00
45:
45: There were 2 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
45: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.434 0.217 199.7
45: (ns/day) (hour/ns)
45: Performance: 6.754 3.553
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'Argon'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.474 0.237 199.9
45: (ns/day) (hour/ns)
45: Performance: 6.194 3.875
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_3_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/3 (547 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.537 0.269 199.8
45: (ns/day) (hour/ns)
45: Performance: 5.462 4.394
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.445 0.223 199.9
45: (ns/day) (hour/ns)
45: Performance: 6.592 3.641
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_4_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/4 (4884 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: NVE simulation: will use the initial temperature of 398.997 K for
45: determining the Verlet buffer size
45:
45:
45: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 4 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
45: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 1.188 0.595 199.9
45: (ns/day) (hour/ns)
45: Performance: 2.471 9.714
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Can not increase nstlist because an NVE ensemble is used
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.547 0.274 199.8
45: (ns/day) (hour/ns)
45: Performance: 5.369 4.470
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_5_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/5 (5276 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.497 0.249 199.8
45: (ns/day) (hour/ns)
45: Performance: 5.906 4.064
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.393 0.196 199.8
45: (ns/day) (hour/ns)
45: Performance: 7.478 3.209
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_6_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/6 (5220 ms)
45: [ RUN ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7
45:
45: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
45: that with the Verlet scheme, nstlist has no effect on the accuracy of
45: your simulation.
45:
45:
45: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: Setting nstcalcenergy (100) equal to nstenergy (4)
45:
45: Generated 330891 of the 330891 non-bonded parameter combinations
45: Generating 1-4 interactions: fudge = 0.5
45: Generated 330891 of the 330891 1-4 parameter combinations
45: Excluding 2 bonded neighbours molecule type 'SOL'
45: Number of degrees of freedom in T-Coupling group System is 27.00
45:
45: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_input.mdp]:
45: You are using a plain Coulomb cut-off, which might produce artifacts.
45: You might want to consider using PME electrostatics.
45:
45:
45:
45: There were 3 notes
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
45: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
45: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
45: Note that mdrun will redetermine rlist based on the actual pair-list setup
45: This run will generate roughly 0 Mb of data
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.490 0.245 199.8
45: (ns/day) (hour/ns)
45: Performance: 5.983 4.011
45: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
45: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
45: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
45:
45: Using 1 MPI thread
45: Using 2 OpenMP threads
45:
45:
45: NOTE: The number of threads is not equal to the number of (logical) cores
45: and the -pin option is set to auto: will not pin threads to cores.
45: This can lead to significant performance degradation.
45: Consider using -pin on (and -pinoffset in case you run multiple jobs).
45:
45: WARNING: Using the slow plain C kernels. This should
45: not happen during routine usage on supported platforms.
45: starting mdrun 'spc2'
45: 16 steps, 0.0 ps.
45:
45: Writing final coordinates.
45:
45: Core t (s) Wall t (s) (%)
45: Time: 0.459 0.230 199.9
45: (ns/day) (hour/ns)
45: Performance: 6.399 3.750
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim1.edr as double precision energy file
45: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/SimulatorsAreEquivalentDefaultLegacy_SimulatorComparisonTest_WithinTolerances_7_sim2.edr as double precision energy file
45:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
45:
45: [ OK ] SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest.WithinTolerances/7 (5040 ms)
45: [----------] 8 tests from SimulatorsAreEquivalentDefaultLegacy/SimulatorComparisonTest (22464 ms total)
45:
45: [----------] Global test environment tear-down
45: [==========] 24 tests from 7 test cases ran. (51110 ms total)
45: [ PASSED ] 24 tests.
45/54 Test #45: MdrunTests .......................... Passed 51.20 sec
test 46
Start 46: MdrunNonIntegratorTests
46: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-non-integrator-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunNonIntegratorTests.xml"
46: Test timeout computed to be: 600
46: [==========] Running 65 tests from 7 test cases.
46: [----------] Global test environment set-up.
46: [----------] 1 test from NonbondedBenchTest
46: [ RUN ] NonbondedBenchTest.BasicEndToEndTest
46: System size: 3000 atoms
46: Cut-off radius: 1 nm
46: Number of threads: 1
46: Number of iterations: 1
46: Compute energies: no
46: Ewald excl. corr.: analytical
46:
46: Coulomb LJ comb. SIMD Mcycles Mcycles/it. pairs/cycle
46: total useful
46: Ewald all geom. no 0.000 0.0000 inf inf
46: [ OK ] NonbondedBenchTest.BasicEndToEndTest (723 ms)
46: [----------] 1 test from NonbondedBenchTest (723 ms total)
46:
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -4.79910463671071e+01
46: Maximum force = 1.86297359432220e+02 on atom 13
46: Norm of force = 8.77219865482161e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (4102 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 3.02331e+02 on atom 3
46: F-Norm = 1.18024e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -5.58622538633290e+01
46: Maximum force = 4.27274822366523e+02 on atom 13
46: Norm of force = 1.84530029253828e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (4147 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19376899751521e+02
46: Maximum force = 9.99884921009767e+03 on atom 9
46: Norm of force = 4.61669565054298e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (1064 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46:
46: NOTE 3 [file glycine_vacuo.top, line 12]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Number of degrees of freedom in T-Coupling group System is 22.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41575e+04 on atom 10
46: F-Norm = 1.18451e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.51743018140925e+02
46: Maximum force = 7.42089573409111e+03 on atom 9
46: Norm of force = 3.56929298615739e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (1068 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.56984193848276e+02
46: Maximum force = 4.56923624626296e+02 on atom 17
46: Norm of force = 1.83258377168331e+02
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (126 ms)
46: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46:
46: NOTE 4 [file unknown]:
46: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 1.06800e+03 on atom 28
46: F-Norm = 4.26922e+02
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = -1.69410778678185e+02
46: Maximum force = 2.18225948473957e+02 on atom 17
46: Norm of force = 7.92068036537697e+01
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
46: This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (128 ms)
46: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (10637 ms total)
46:
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents converged to Fmax < 10 in 1 steps
46: Potential Energy = -9.74257075835450e-01
46: Maximum force = 4.01322929015108e+00 on atom 1
46: Norm of force = 1.63839399694368e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (36 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.90642313893957e-01
46: Maximum force = 2.57812909491105e+00 on atom 1
46: Norm of force = 1.05251679559258e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (37 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 4.01323e+00 on atom 1
46: F-Norm = 1.63839e+00
46:
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer converged to Fmax < 10 in 0 steps
46: Potential Energy = -9.90642313893957e-01
46: Maximum force = 2.57812909491105e+00 on atom 1
46: Norm of force = 1.05251679559258e+00
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (36 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Steepest Descents:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Steepest Descents did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 3.19395484891517e+02
46: Maximum force = 9.97041707197910e+03 on atom 9
46: Norm of force = 4.62274878665467e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (1095 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Polak-Ribiere Conjugate Gradients:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 1.56258793899479e+02
46: Maximum force = 7.50181017480397e+03 on atom 9
46: Norm of force = 3.61390332564874e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (1081 ms)
46: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46:
46: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Glycine'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46:
46: There was 1 warning
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: L-BFGS minimization only supports a single rank. Choosing to use only a single thread-MPI rank.
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Low-Memory BFGS Minimizer:
46: Tolerance (Fmax) = 1.00000e+01
46: Number of steps = 4
46: Using 10 BFGS correction steps.
46:
46: F-max = 2.41672e+04 on atom 10
46: F-Norm = 1.19357e+04
46:
46:
46: Energy minimization reached the maximum number of steps before the forces
46: reached the requested precision Fmax < 10.
46:
46: writing lowest energy coordinates.
46:
46: Low-Memory BFGS Minimizer did not converge to Fmax < 10 in 5 steps.
46: Potential Energy = 5.61116097794203e+02
46: Maximum force = 1.26854826291223e+04 on atom 10
46: Norm of force = 6.06436286976271e+03
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
46: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1103 ms)
46: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (3388 ms total)
46:
46: [----------] 5 tests from NormalModesWorks/NormalModesTest
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 3 of the 3 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation '2 scaled waters'
46: 12 steps.
46:
46: Maximum force: 9.96989e-06
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.6-Raspbian-2020.6-2
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/0 (88 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 20503 of the 20503 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 1
46: Generated 17396 of the 20503 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
46:
46: NOTE 3 [file villin.top, line 2452]:
46: System has non-zero total charge: -2.000000
46: Total charge should normally be an integer. See
46: http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
46: for discussion on how close it should be to an integer.
46:
46:
46:
46: Number of degrees of freedom in T-Coupling group System is 765.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=256), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'AMYLOID BETA A4 PROTEIN'
46: 512 steps.
46:
46: Maximum force: 6.97568e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.6-Raspbian-2020.6-2
46:
46: Diagonalizing to find vectors 7 through 50...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--50 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 256 Atoms
46: Using begin = 7 and end = 50
46: Full matrix storage format, nrow=768, ncols=768
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/1 (22190 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'flex spc dimer'
46: 12 steps.
46:
46: Maximum force: 3.36401e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.6-Raspbian-2020.6-2
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/2 (4464 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
46: nstcomm to nstcalcenergy
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Number of degrees of freedom in T-Coupling group System is 6.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=3), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation '1 TIP5P'
46: 6 steps.
46:
46: Maximum force: 2.42882e-04
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.6-Raspbian-2020.6-2
46:
46: Diagonalizing to find vectors 7 through 9...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--9 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 3 Atoms
46: There are: 2 VSites
46: Using begin = 7 and end = 9
46: Full matrix storage format, nrow=9, ncols=9
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/3 (4404 ms)
46: [ RUN ] NormalModesWorks/NormalModesTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 6 of the 10 non-bonded parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SW'
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Number of degrees of freedom in T-Coupling group System is 15.00
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46:
46: Small system size (N=6), using full Hessian format.
46: Allocating Hessian memory...
46:
46: starting normal mode calculation 'sw dimer'
46: 12 steps.
46:
46: Maximum force: 1.07599e-03
46: The force is probably not small enough to ensure that you are at a minimum.
46: Be aware that negative eigenvalues may occur
46: when the resulting matrix is diagonalized.
46:
46:
46: Writing Hessian...
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalModesWorks_NormalModesTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Reading double precision matrix generated by GROMACS 2020.6-Raspbian-2020.6-2
46:
46: Diagonalizing to find vectors 7 through 18...
46: Writing eigenvalues...
46:
46: Writing average structure & eigenvectors 7--18 to eigenvec.trr
46: This run will generate roughly 0 Mb of data
46: There are: 6 Atoms
46: There are: 2 Shells
46: There are: 2 VSites
46:
46: NOTE: in the current version shell prediction during the crun is disabled
46:
46: Using begin = 7 and end = 18
46: Full matrix storage format, nrow=18, ncols=18
46: Writing eigenfrequencies - negative eigenvalues will be set to zero.
46: Cannot compute entropy when -first = 7
46: [ OK ] NormalModesWorks/NormalModesTest.WithinTolerances/4 (99 ms)
46: [----------] 5 tests from NormalModesWorks/NormalModesTest (31246 ms total)
46:
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.378 0.189 199.8
46: (ns/day) (hour/ns)
46: Performance: 7.769 3.089
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.trr'
46:
46: trr version: GMX_trn_file (double precision)
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.006 0.003 193.7
46: (ns/day) (hour/ns)
46: Performance: 439.101 0.055
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_0_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/0 (245 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 68.810 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.422 0.211 199.9
46: (ns/day) (hour/ns)
46: Performance: 6.962 3.447
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.003 193.7
46: (ns/day) (hour/ns)
46: Performance: 435.778 0.055
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_1_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/1 (267 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.708 nm, buffer size 0.008 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.708 nm, buffer size 0.008 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.419 0.210 199.8
46: (ns/day) (hour/ns)
46: Performance: 7.000 3.428
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.708 to 0.73
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.006 0.003 193.3
46: (ns/day) (hour/ns)
46: Performance: 448.108 0.054
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_2_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/2 (267 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 1 of the 1 non-bonded parameter combinations
46: Excluding 1 bonded neighbours molecule type 'Argon'
46: Number of degrees of freedom in T-Coupling group System is 33.00
46:
46: There were 2 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Argon'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
46: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.418 0.209 199.8
46: (ns/day) (hour/ns)
46: Performance: 7.015 3.421
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Argon', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.036 0.018 198.8
46: (ns/day) (hour/ns)
46: Performance: 82.094 0.292
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_3_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/3 (292 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.435 0.218 199.7
46: (ns/day) (hour/ns)
46: Performance: 6.746 3.558
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.7
46: (ns/day) (hour/ns)
46: Performance: 391.596 0.061
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_4_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/4 (4689 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 398.997 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
46: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.433 0.217 199.9
46: (ns/day) (hour/ns)
46: Performance: 6.781 3.539
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.6
46: (ns/day) (hour/ns)
46: Performance: 398.951 0.060
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_5_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/5 (4622 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.735 nm, buffer size 0.035 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.733 nm, buffer size 0.033 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.388 0.194 199.7
46: (ns/day) (hour/ns)
46: Performance: 7.565 3.172
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.733 to 0.824
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.9
46: (ns/day) (hour/ns)
46: Performance: 382.432 0.063
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_6_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/6 (4702 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 330891 of the 330891 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 330891 of the 330891 1-4 parameter combinations
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 27.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'spc2'
46: 16 steps, 0.0 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.493 0.247 199.8
46: (ns/day) (hour/ns)
46: Performance: 5.946 4.036
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'spc2', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.007 0.004 193.7
46: (ns/day) (hour/ns)
46: Performance: 388.804 0.062
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_7_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/7 (4654 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.449 0.225 199.7
46: (ns/day) (hour/ns)
46: Performance: 6.540 3.670
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 196.6
46: (ns/day) (hour/ns)
46: Performance: 152.065 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_8_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/8 (425 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 456.887 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 6 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 6 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 456.887 K
46: Calculated rlist for 1x1 atom pair-list as 0.737 nm, buffer size 0.037 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.734 nm, buffer size 0.034 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.520 0.260 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.644 4.252
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 195.3
46: (ns/day) (hour/ns)
46: Performance: 208.876 0.115
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_9_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/9 (469 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.748 nm, buffer size 0.048 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.744 nm, buffer size 0.044 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.476 0.239 199.7
46: (ns/day) (hour/ns)
46: Performance: 6.156 3.898
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 100, rlist from 0.744 to 0.868
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 195.2
46: (ns/day) (hour/ns)
46: Performance: 211.872 0.113
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_10_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/10 (563 ms)
46: [ RUN ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2145 of the 2145 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2145 of the 2145 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
46:
46: NOTE 3 [file unknown]:
46: You are using constraints on all bonds, whereas the forcefield has been
46: parametrized only with constraints involving hydrogen atoms. We suggest
46: using constraints = h-bonds instead, this will also improve performance.
46:
46: Cleaning up constraints and constant bonded interactions with virtual sites
46: Removed 18 Angles with virtual sites, 21 left
46: Removed 10 Proper Dih.s with virtual sites, 44 left
46: Converted 15 Constraints with virtual sites to connections, 7 left
46: Number of degrees of freedom in T-Coupling group System is 23.00
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: There are 9 non-linear virtual site constructions. Their contribution to
46: the energy error is approximated. In most cases this does not affect the
46: error significantly.
46:
46:
46: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 5 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'Alanine dipeptide in vacuo'
46: 16 steps, 0.0 ps.
46: turning all bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.729 nm, buffer size 0.029 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.726 nm, buffer size 0.026 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.513 0.257 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.721 4.195
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 40, rlist from 0.726 to 0.869
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun 'Alanine dipeptide in vacuo', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.014 0.007 195.5
46: (ns/day) (hour/ns)
46: Performance: 208.234 0.115
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/NormalMdrunIsReproduced_MdrunRerunTest_WithinTolerances_11_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] NormalMdrunIsReproduced/MdrunRerunTest.WithinTolerances/11 (559 ms)
46: [----------] 12 tests from NormalMdrunIsReproduced/MdrunRerunTest (21756 ms total)
46:
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.567 0.284 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.177 4.636
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.9
46: (ns/day) (hour/ns)
46: Performance: 152.102 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_0_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/0 (470 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.617 0.309 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.753 5.049
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 190.8
46: (ns/day) (hour/ns)
46: Performance: 152.929 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_1_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/1 (495 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.551 0.276 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.325 4.507
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 189.0
46: (ns/day) (hour/ns)
46: Performance: 150.280 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_2_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/2 (501 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.495 0.248 199.6
46: (ns/day) (hour/ns)
46: Performance: 5.928 4.049
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 187.8
46: (ns/day) (hour/ns)
46: Performance: 151.896 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_3_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/3 (433 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.561 0.281 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.224 4.594
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.6
46: (ns/day) (hour/ns)
46: Performance: 150.163 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_4_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/4 (467 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.572 0.286 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.129 4.679
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.9
46: (ns/day) (hour/ns)
46: Performance: 150.086 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_5_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/5 (522 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.561 0.281 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.230 4.589
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.8
46: (ns/day) (hour/ns)
46: Performance: 151.199 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_6_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/6 (467 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.588 0.295 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.986 4.814
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.8
46: (ns/day) (hour/ns)
46: Performance: 150.928 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_7_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/7 (508 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.559 0.280 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.251 4.570
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.8
46: (ns/day) (hour/ns)
46: Performance: 150.640 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_8_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/8 (514 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.648 0.324 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.527 5.301
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 189.1
46: (ns/day) (hour/ns)
46: Performance: 150.273 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_9_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/9 (511 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.583 0.292 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.030 4.772
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 190.1
46: (ns/day) (hour/ns)
46: Performance: 151.444 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_10_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/10 (493 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.687 0.344 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.273 5.617
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 190.9
46: (ns/day) (hour/ns)
46: Performance: 151.571 0.158
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_11_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/11 (542 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.600 0.300 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.892 4.906
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 189.9
46: (ns/day) (hour/ns)
46: Performance: 150.306 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_12_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/12 (490 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.612 0.306 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.801 4.999
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 189.2
46: (ns/day) (hour/ns)
46: Performance: 148.505 0.162
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_13_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/13 (544 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.555 0.278 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.292 4.535
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.7
46: (ns/day) (hour/ns)
46: Performance: 152.396 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_14_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/14 (468 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.530 0.265 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.543 4.330
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.0
46: (ns/day) (hour/ns)
46: Performance: 150.240 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_15_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/15 (479 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.590 0.295 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.973 4.826
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 189.0
46: (ns/day) (hour/ns)
46: Performance: 146.677 0.164
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_16_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/16 (542 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.554 0.277 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.296 4.532
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 189.1
46: (ns/day) (hour/ns)
46: Performance: 149.395 0.161
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_17_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/17 (467 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.624 0.312 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.705 5.101
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 187.2
46: (ns/day) (hour/ns)
46: Performance: 148.091 0.162
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_18_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/18 (509 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.595 0.298 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.932 4.866
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.9
46: (ns/day) (hour/ns)
46: Performance: 150.010 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_19_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/19 (513 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.576 0.288 199.9
46: (ns/day) (hour/ns)
46: Performance: 5.094 4.711
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.8
46: (ns/day) (hour/ns)
46: Performance: 150.064 0.160
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_20_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/20 (477 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: NVE simulation: will use the initial temperature of 293.480 K for
46: determining the Verlet buffer size
46:
46:
46: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 4 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 293.48 K
46: Calculated rlist for 1x1 atom pair-list as 0.751 nm, buffer size 0.051 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.748 nm, buffer size 0.048 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.626 0.313 199.9
46: (ns/day) (hour/ns)
46: Performance: 4.692 5.115
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 190.1
46: (ns/day) (hour/ns)
46: Performance: 149.330 0.161
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_21_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/21 (511 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.688 0.344 199.8
46: (ns/day) (hour/ns)
46: Performance: 4.265 5.628
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 190.2
46: (ns/day) (hour/ns)
46: Performance: 148.027 0.162
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_22_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/22 (641 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.550 0.275 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.331 4.502
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 190.9
46: (ns/day) (hour/ns)
46: Performance: 150.534 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_23_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/23 (604 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.585 0.293 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.013 4.788
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 188.8
46: (ns/day) (hour/ns)
46: Performance: 147.889 0.162
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_24_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/24 (607 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.518 0.259 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.664 4.237
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 188.9
46: (ns/day) (hour/ns)
46: Performance: 145.651 0.165
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_25_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/25 (598 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.498 0.249 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.895 4.071
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.019 0.010 188.9
46: (ns/day) (hour/ns)
46: Performance: 148.266 0.162
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_26_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/26 (602 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: Non-default thread affinity set probably by the OpenMP library,
46: disabling internal thread affinity
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.552 0.276 199.7
46: (ns/day) (hour/ns)
46: Performance: 5.317 4.514
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.7
46: (ns/day) (hour/ns)
46: Performance: 150.951 0.159
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_27_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/27 (579 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.640 0.321 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.582 5.237
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.5
46: (ns/day) (hour/ns)
46: Performance: 152.516 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_28_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/28 (674 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.651 0.326 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.509 5.322
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.018 0.010 188.5
46: (ns/day) (hour/ns)
46: Performance: 152.558 0.157
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_29_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/29 (621 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.801 0.401 199.8
46: (ns/day) (hour/ns)
46: Performance: 3.662 6.554
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.017 0.009 188.3
46: (ns/day) (hour/ns)
46: Performance: 158.268 0.152
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_30_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/30 (726 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.646 0.324 199.7
46: (ns/day) (hour/ns)
46: Performance: 4.540 5.287
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.017 0.009 188.2
46: (ns/day) (hour/ns)
46: Performance: 158.893 0.151
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_31_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/31 (618 ms)
46: [ RUN ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46:
46: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: Setting nstcalcenergy (100) equal to nstenergy (4)
46:
46: Generated 2485 of the 2485 non-bonded parameter combinations
46: Generating 1-4 interactions: fudge = 0.5
46: Generated 2485 of the 2485 1-4 parameter combinations
46: Excluding 3 bonded neighbours molecule type 'nonanol'
46: Excluding 2 bonded neighbours molecule type 'SOL'
46: Number of degrees of freedom in T-Coupling group System is 79.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_input.mdp]:
46: You are using a plain Coulomb cut-off, which might produce artifacts.
46: You might want to consider using PME electrostatics.
46:
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun '30 system in water'
46: 16 steps, 0.0 ps.
46: turning H bonds into constraints...
46: turning H bonds into constraints...
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
46: Calculated rlist for 1x1 atom pair-list as 0.752 nm, buffer size 0.052 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.749 nm, buffer size 0.049 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.698 0.349 199.8
46: (ns/day) (hour/ns)
46: Performance: 4.205 5.707
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Changing nstlist from 8 to 25, rlist from 0.749 to 0.88
46:
46: Using 1 MPI thread
46: Using 2 OpenMP threads
46:
46:
46: NOTE: The number of threads is not equal to the number of (logical) cores
46: and the -pin option is set to auto: will not pin threads to cores.
46: This can lead to significant performance degradation.
46: Consider using -pin on (and -pinoffset in case you run multiple jobs).
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting md rerun '30 system in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.trr'
46:
46:
Reading frame 0 time 0.000
Reading frame 1 time 0.004
Reading frame 2 time 0.008
Reading frame 3 time 0.012
Reading frame 4 time 0.016
Last frame 4 time 0.016
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.017 0.009 188.2
46: (ns/day) (hour/ns)
46: Performance: 158.264 0.152
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim1.edr as double precision energy file
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MdrunIsReproduced_MdrunRerunFreeEnergyTest_WithinTolerances_32_sim2.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
Last energy frame read 4 time 0.016
46:
46: [ OK ] MdrunIsReproduced/MdrunRerunFreeEnergyTest.WithinTolerances/32 (644 ms)
46: [----------] 33 tests from MdrunIsReproduced/MdrunRerunFreeEnergyTest (17841 ms total)
46:
46: [----------] 2 tests from Angles1/SimpleMdrunTest
46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/0
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Excluding 3 bonded neighbours molecule type 'butane'
46:
46: NOTE 2 [file angles1.top, line 72]:
46: In moleculetype 'butane' 4 atoms are not bound by a potential or
46: constraint to any other atom in the same moleculetype. Although
46: technically this might not cause issues in a simulation, this often means
46: that the user forgot to add a bond/potential/constraint or put multiple
46: molecules in the same moleculetype definition by mistake. Run with -v to
46: get information for each atom.
46:
46: Number of degrees of freedom in T-Coupling group System is 9.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0_input.mdp]:
46: NVE simulation: will use the initial temperature of 238.919 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'This_incredible_box_of_butane'
46: 50 steps, 0.1 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.436 0.218 199.8
46: (ns/day) (hour/ns)
46: Performance: 20.206 1.188
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_0.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/0 (281 ms)
46: [ RUN ] Angles1/SimpleMdrunTest.WithinTolerances/1
46:
46: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
46: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
46: that with the Verlet scheme, nstlist has no effect on the accuracy of
46: your simulation.
46:
46: Generated 3 of the 3 non-bonded parameter combinations
46: Excluding 3 bonded neighbours molecule type 'butane'
46:
46: NOTE 2 [file angles1.top, line 72]:
46: In moleculetype 'butane' 4 atoms are not bound by a potential or
46: constraint to any other atom in the same moleculetype. Although
46: technically this might not cause issues in a simulation, this often means
46: that the user forgot to add a bond/potential/constraint or put multiple
46: molecules in the same moleculetype definition by mistake. Run with -v to
46: get information for each atom.
46:
46: Number of degrees of freedom in T-Coupling group System is 9.00
46:
46: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1_input.mdp]:
46: NVE simulation: will use the initial temperature of 238.919 K for
46: determining the Verlet buffer size
46:
46:
46: There were 3 notes
46: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
46: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
46: Can not increase nstlist because an NVE ensemble is used
46: Using 1 MPI thread
46:
46: Non-default thread affinity set, disabling internal thread affinity
46:
46: Using 2 OpenMP threads
46:
46:
46: WARNING: Using the slow plain C kernels. This should
46: not happen during routine usage on supported platforms.
46: starting mdrun 'This_incredible_box_of_butane'
46: 50 steps, 0.1 ps.
46: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 238.919 K
46: Calculated rlist for 1x1 atom pair-list as 0.700 nm, buffer size 0.000 nm
46: Set rlist, assuming 4x4 atom pair-list, to 0.700 nm, buffer size 0.000 nm
46: Note that mdrun will redetermine rlist based on the actual pair-list setup
46: This run will generate roughly 0 Mb of data
46:
46: Writing final coordinates.
46:
46: Core t (s) Wall t (s) (%)
46: Time: 0.451 0.226 199.9
46: (ns/day) (hour/ns)
46: Performance: 19.528 1.229
46: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Angles1_SimpleMdrunTest_WithinTolerances_1.edr as double precision energy file
46:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 5 time 0.020
Reading energy frame 6 time 0.024
Reading energy frame 7 time 0.028
Reading energy frame 8 time 0.032
Reading energy frame 9 time 0.036
Reading energy frame 10 time 0.040
Reading energy frame 11 time 0.044
Reading energy frame 12 time 0.048
Reading energy frame 13 time 0.050
Last energy frame read 13 time 0.050
46: [ OK ] Angles1/SimpleMdrunTest.WithinTolerances/1 (294 ms)
46: [----------] 2 tests from Angles1/SimpleMdrunTest (576 ms total)
46:
46: [----------] Global test environment tear-down
46: [==========] 65 tests from 7 test cases ran. (86170 ms total)
46: [ PASSED ] 65 tests.
46/54 Test #46: MdrunNonIntegratorTests ............. Passed 86.36 sec
test 47
Start 47: MdrunTpiTests
47: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-tpi-test "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunTpiTests.xml"
47: Test timeout computed to be: 600
47: [==========] Running 2 tests from 1 test case.
47: [----------] Global test environment set-up.
47: [----------] 2 tests from Simple/TpiTest
47: [ RUN ] Simple/TpiTest.ReproducesOutput/0
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 8.706e+02 <mu> 8.706e+02
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/0 (5022 ms)
47: [ RUN ] Simple/TpiTest.ReproducesOutput/1
47: Ignoring obsolete mdp entry 'ns_type'
47: Generated 331705 of the 331705 non-bonded parameter combinations
47: Generating 1-4 interactions: fudge = 0.5
47: Generated 331705 of the 331705 1-4 parameter combinations
47: Excluding 2 bonded neighbours molecule type 'SOL'
47: Excluding 3 bonded neighbours molecule type 'methane'
47: Number of degrees of freedom in T-Coupling group System is 1308.00
47: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
47: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/Simple_TpiTest_ReproducesOutput_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
47: TPI is not implemented for GPUs.
47:
47: Using 1 MPI thread
47: Using 1 OpenMP thread
47:
47:
47: NOTE: Thread affinity was not set.
47:
47: WARNING: Using the slow plain C kernels. This should
47: not happen during routine usage on supported platforms.
47: Reading frames from gro file '216 water molecules', 648 atoms.
47:
Reading frame 0 time 0.000 mu 9.144e+01 <mu> 9.144e+01
47:
Last frame 0 time 0.000
47: Analysing residue names:
47: There are: 216 Water residues
47: There are: 1 Other residues
47: Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
47: This run will generate roughly 0 Mb of data
47: [ OK ] Simple/TpiTest.ReproducesOutput/1 (5071 ms)
47: [----------] 2 tests from Simple/TpiTest (10093 ms total)
47:
47: [----------] Global test environment tear-down
47: [==========] 2 tests from 1 test case ran. (10093 ms total)
47: [ PASSED ] 2 tests.
47/54 Test #47: MdrunTpiTests ....................... Passed 10.17 sec
test 48
Start 48: MdrunMpiTests
48: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiTests.xml"
48: Test timeout computed to be: 600
48: [==========] Running 22 tests from 7 test cases.
48: [----------] Global test environment set-up.
48: [----------] 1 test from DomainDecompositionSpecialCasesTest
48: [ RUN ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -545458947
48: Generated 3 of the 3 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 3 of the 3 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 9.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/DomainDecompositionSpecialCasesTest_AnEmptyDomainWorks.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc2'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.007 0.002 325.7
48: (ns/day) (hour/ns)
48: Performance: 41.866 0.573
48: This run will generate roughly 0 Mb of data
48: [ OK ] DomainDecompositionSpecialCasesTest.AnEmptyDomainWorks (83 ms)
48: [----------] 1 test from DomainDecompositionSpecialCasesTest (83 ms total)
48:
48: [----------] 4 tests from MimicTest
48: [ RUN ] MimicTest.OneQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -67440649
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.620 0.685 382.5
48: (ns/day) (hour/ns)
48: Performance: 0.126 190.269
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_OneQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.OneQuantumMol (2110 ms)
48: [ RUN ] MimicTest.AllQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -210386946
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.520 0.660 381.8
48: (ns/day) (hour/ns)
48: Performance: 0.131 183.325
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_AllQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.AllQuantumMol (2048 ms)
48: [ RUN ] MimicTest.TwoQuantumMol
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -545620097
48: Generated 10 of the 10 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 10 of the 10 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 21.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: NVE simulation with an initial temperature of zero: will use a Verlet
48: buffer of 10%. Check your energy drift!
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'Generated by gmx solvate', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/4water.gro'
48:
48: Reading frames from gro file 'Generated by gmx solvate', 12 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.520 0.660 381.9
48: (ns/day) (hour/ns)
48: Performance: 0.131 183.325
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_TwoQuantumMol.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.TwoQuantumMol (2055 ms)
48: [ RUN ] MimicTest.BondCuts
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -359682306
48: Generated 2211 of the 2211 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2211 of the 2211 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
48: Number of degrees of freedom in T-Coupling group rest is 66.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: NVE simulation: will use the initial temperature of 300.368 K for
48: determining the Verlet buffer size
48:
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting md rerun 'UNNAMED in water', reading coordinates from input trajectory '/<<PKGBUILDDIR>>/src/testutils/simulationdatabase/ala.gro'
48:
48: Reading frames from gro file 'Alanine dipeptide in water', 23 atoms.
48:
Reading frame 0 time 0.000
Last frame 0 time 0.000
48:
48: Core t (s) Wall t (s) (%)
48: Time: 2.480 0.650 381.5
48: (ns/day) (hour/ns)
48: Performance: 0.133 180.539
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MimicTest_BondCuts.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300.368 K
48: Calculated rlist for 1x1 atom pair-list as 1.034 nm, buffer size 0.034 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.025 nm, buffer size 0.025 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: This run will generate roughly 0 Mb of data
48: [ OK ] MimicTest.BondCuts (2149 ms)
48: [----------] 4 tests from MimicTest (8362 ms total)
48:
48: [----------] 1 test from MultiSimTerminationTest
48: [ RUN ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] MultiSimTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from MultiSimTerminationTest (0 ms total)
48:
48: [----------] 3 tests from PmeTest
48: [ RUN ] PmeTest.ReproducesEnergies
48: Setting the LD random seed to -295973221
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
48: This run will generate roughly 0 Mb of data
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 8.887 2.260 393.3
48: (ns/day) (hour/ns)
48: Performance: 0.803 29.891
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeAuto.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 8.837 2.250 392.8
48: (ns/day) (hour/ns)
48: Performance: 0.806 29.759
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.
48: starting mdrun 'spc-and-methanol'
48: 20 steps, 0.0 ps.
48:
48: Writing final coordinates.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 8.902 2.265 393.1
48: (ns/day) (hour/ns)
48: Performance: 0.801 29.956
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ReproducesEnergies_spc-and-methanol_PmeOnCpuTune.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.001
Reading energy frame 2 time 0.002
Reading energy frame 3 time 0.003
Reading energy frame 4 time 0.004
Reading energy frame 5 time 0.005
Reading energy frame 6 time 0.006
Reading energy frame 7 time 0.007
Reading energy frame 8 time 0.008
Reading energy frame 9 time 0.009
Reading energy frame 10 time 0.010
Reading energy frame 11 time 0.011
Reading energy frame 12 time 0.012
Reading energy frame 13 time 0.013
Reading energy frame 14 time 0.014
Reading energy frame 15 time 0.015
Reading energy frame 16 time 0.016
Reading energy frame 17 time 0.017
Reading energy frame 18 time 0.018
Reading energy frame 19 time 0.019
Reading energy frame 20 time 0.020
Last energy frame read 20 time 0.020 [ OK ] PmeTest.ReproducesEnergies (9605 ms)
48: [ RUN ] PmeTest.ScalesTheBox
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to -348153089
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group rest is 12.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: NVE simulation: will use the initial temperature of 1046.791 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.431 0.150 287.5
48: (ns/day) (hour/ns)
48: Performance: 0.577 41.603
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBox_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 1046.79 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x28, spacing 0.107 0.107 0.107
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBox (1102 ms)
48: [ RUN ] PmeTest.ScalesTheBoxWithWalls
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: For a correct single-point energy evaluation with nsteps = 0, use
48: continuation = yes to avoid constraining the input coordinates.
48:
48: Setting the LD random seed to 503296597
48: Generated 8 of the 10 non-bonded parameter combinations
48: Excluding 2 bonded neighbours molecule type 'Methanol'
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Searching the wall atom type(s)
48: Number of degrees of freedom in T-Coupling group rest is 13.00
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: NVE simulation: will use the initial temperature of 966.268 K for
48: determining the Verlet buffer size
48:
48: Estimate for the relative computational load of the PME mesh part: 1.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_input.mdp]:
48: The optimal PME mesh load for parallel simulations is below 0.5
48: and for highly parallel simulations between 0.25 and 0.33,
48: for higher performance, increase the cut-off and the PME grid spacing.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Can not increase nstlist because an NVE ensemble is used
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48: Using 0 OpenMP thread per tMPI thread for PME
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48: starting mdrun 'spc-and-methanol'
48: 0 steps, 0.0 ps.
48:
48: Core t (s) Wall t (s) (%)
48: Time: 0.851 0.252 337.2
48: (ns/day) (hour/ns)
48: Performance: 0.342 70.082
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PmeTest_ScalesTheBoxWithWalls_spc-and-methanol_PmeOnCpu.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 966.268 K
48: Calculated rlist for 1x1 atom pair-list as 1.000 nm, buffer size 0.000 nm
48: Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
48: Note that mdrun will redetermine rlist based on the actual pair-list setup
48: Calculating fourier grid dimensions for X Y Z
48: Using a fourier grid of 28x28x128, spacing 0.107 0.107 0.118
48: This run will generate roughly 0 Mb of data
48: [ OK ] PmeTest.ScalesTheBoxWithWalls (1392 ms)
48: [----------] 3 tests from PmeTest (12099 ms total)
48:
48: [----------] 1 test from ReplicaExchangeTerminationTest
48: [ RUN ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts
48: [ OK ] ReplicaExchangeTerminationTest.WritesCheckpointAfterMaxhTerminationAndThenRestarts (0 ms)
48: [----------] 1 test from ReplicaExchangeTerminationTest (0 ms total)
48:
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -4.79910463671071e+01
48: Maximum force = 1.86297359432218e+02 on atom 13
48: Norm of force = 8.77219865482161e+01
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/0 (7198 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 330891 of the 330891 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 330891 of the 330891 1-4 parameter combinations
48: Excluding 2 bonded neighbours molecule type 'SOL'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 3.02331e+02 on atom 3
48: F-Norm = 1.18024e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -5.58622538633290e+01
48: Maximum force = 4.27274822366538e+02 on atom 13
48: Norm of force = 1.84530029253833e+02
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/1 (8790 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.19376899751521e+02
48: Maximum force = 9.99884921009767e+03 on atom 9
48: Norm of force = 4.61669565054298e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_2_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/2 (4281 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48:
48: NOTE 3 [file glycine_vacuo.top, line 12]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Number of degrees of freedom in T-Coupling group System is 22.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41575e+04 on atom 10
48: F-Norm = 1.18451e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.51743018140926e+02
48: Maximum force = 7.42089573409112e+03 on atom 9
48: Norm of force = 3.56929298615739e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning H bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/3 (5838 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 4 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.56984193848276e+02
48: Maximum force = 4.56923624626296e+02 on atom 17
48: Norm of force = 1.83258377168331e+02
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 3.000
Last energy frame read 2 time 3.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/4 (4859 ms)
48: [ RUN ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 2145 of the 2145 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 0.5
48: Generated 2145 of the 2145 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Alanine_dipeptide'
48:
48: NOTE 3 [file unknown]:
48: You are using constraints on all bonds, whereas the forcefield has been
48: parametrized only with constraints involving hydrogen atoms. We suggest
48: using constraints = h-bonds instead, this will also improve performance.
48:
48:
48: NOTE 4 [file unknown]:
48: For accurate cg with LINCS constraints, lincs-order should be 8 or more.
48:
48: Cleaning up constraints and constant bonded interactions with virtual sites
48: Removed 18 Angles with virtual sites, 21 left
48: Removed 10 Proper Dih.s with virtual sites, 44 left
48: Converted 15 Constraints with virtual sites to connections, 7 left
48: Number of degrees of freedom in T-Coupling group System is 23.00
48:
48: NOTE 5 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 5 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 1.06800e+03 on atom 28
48: F-Norm = 4.26922e+02
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = -1.69410778678185e+02
48: Maximum force = 2.18225948474048e+02 on atom 17
48: Norm of force = 7.92068036537643e+01
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWorkWithConstraints_EnergyMinimizationTest_WithinTolerances_5_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 turning all bonds into constraints...
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWorkWithConstraints/EnergyMinimizationTest.WithinTolerances/5 (7191 ms)
48: [----------] 6 tests from MinimizersWorkWithConstraints/EnergyMinimizationTest (38158 ms total)
48:
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents converged to Fmax < 10 in 1 steps
48: Potential Energy = -9.74257075835450e-01
48: Maximum force = 4.01322929015108e+00 on atom 3
48: Norm of force = 1.63839399694368e+00
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_0_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Last energy frame read 0 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/0 (1634 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 4.01323e+00 on atom 3
48: F-Norm = 1.63839e+00
48:
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 0 steps
48: Potential Energy = -9.90642313893957e-01
48: Maximum force = 2.57812909491105e+00 on atom 3
48: Norm of force = 1.05251679559258e+00
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_1_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Last energy frame read 1 time 0.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/1 (2170 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_2_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 1 of the 1 non-bonded parameter combinations
48: Excluding 1 bonded neighbours molecule type 'Argon'
48: Number of degrees of freedom in T-Coupling group System is 33.00
48:
48: There were 2 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/2 (32 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Steepest Descents:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Steepest Descents did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 3.19395484891518e+02
48: Maximum force = 9.97041707197910e+03 on atom 9
48: Norm of force = 4.62274878665467e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_3_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 1.000
Reading energy frame 2 time 2.000
Reading energy frame 3 time 3.000
Reading energy frame 4 time 4.000
Last energy frame read 4 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/3 (4121 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
48: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
48: Using 2 MPI threads
48:
48: Non-default thread affinity set, disabling internal thread affinity
48:
48: Using 2 OpenMP threads per tMPI thread
48:
48:
48: WARNING: Using the slow plain C kernels. This should
48: not happen during routine usage on supported platforms.
48:
48: Polak-Ribiere Conjugate Gradients:
48: Tolerance (Fmax) = 1.00000e+01
48: Number of steps = 4
48: F-max = 2.41672e+04 on atom 10
48: F-Norm = 1.19357e+04
48:
48:
48: Energy minimization reached the maximum number of steps before the forces
48: reached the requested precision Fmax < 10.
48:
48: writing lowest energy coordinates.
48:
48: Polak-Ribiere Conjugate Gradients did not converge to Fmax < 10 in 5 steps.
48: Potential Energy = 1.56258793899479e+02
48: Maximum force = 7.50181017480397e+03 on atom 9
48: Norm of force = 3.61390332564874e+03
48: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_4_minimize.edr as double precision energy file
48:
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.000
Reading energy frame 2 time 4.000
Last energy frame read 2 time 4.000 This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/4 (5559 ms)
48: [ RUN ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5
48:
48: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
48: that with the Verlet scheme, nstlist has no effect on the accuracy of
48: your simulation.
48:
48:
48: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting
48: nstcomm to nstcalcenergy
48:
48:
48: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: For efficient BFGS minimization, use switch/shift/pme instead of cut-off.
48:
48: Generated 20503 of the 20503 non-bonded parameter combinations
48: Generating 1-4 interactions: fudge = 1
48: Generated 17396 of the 20503 1-4 parameter combinations
48: Excluding 3 bonded neighbours molecule type 'Glycine'
48: Number of degrees of freedom in T-Coupling group System is 27.00
48:
48: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/MinimizersWork_EnergyMinimizationTest_WithinTolerances_5_input.mdp]:
48: You are using a plain Coulomb cut-off, which might produce artifacts.
48: You might want to consider using PME electrostatics.
48:
48:
48:
48: There were 3 notes
48:
48: There was 1 warning
48: This run will generate roughly 0 Mb of data
48: [ OK ] MinimizersWork/EnergyMinimizationTest.WithinTolerances/5 (1105 ms)
48: [----------] 6 tests from MinimizersWork/EnergyMinimizationTest (14628 ms total)
48:
48: [----------] Global test environment tear-down
48: [==========] 22 tests from 7 test cases ran. (73336 ms total)
48: [ PASSED ] 22 tests.
48:
48: YOU HAVE 4 DISABLED TESTS
48:
48/54 Test #48: MdrunMpiTests ....................... Passed 73.43 sec
test 49
Start 49: MdrunMpiCoordinationTestsOneRank
49: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "1" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsOneRank.xml"
49: Test timeout computed to be: 960
49: [==========] Running 27 tests from 3 test cases.
49: [----------] Global test environment set-up.
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest
49: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.496 0.497 100.0
49: (ns/day) (hour/ns)
49: Performance: 2.958 8.115
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.235 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.253 3.838
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.246 0.247 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.955 4.030
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.205 0.206 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.145 3.359
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.208 0.208 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.063 3.398
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.196 0.197 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.461 3.217
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1859 ms)
49: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1859 ms total)
49:
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.191 0.192 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.667 3.130
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.199 0.200 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.359 3.261
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.249 0.250 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.879 4.082
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.205 0.206 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.147 3.358
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.186 0.187 99.7
49: (ns/day) (hour/ns)
49: Performance: 7.872 3.049
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.234 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.287 3.818
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1487 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.240 0.240 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.112 3.926
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.258 0.259 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.676 4.229
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.241 0.241 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.092 3.940
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.230 0.232 99.5
49: (ns/day) (hour/ns)
49: Performance: 6.344 3.783
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.266 0.268 99.5
49: (ns/day) (hour/ns)
49: Performance: 5.488 4.373
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.276 0.276 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.317 4.514
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1759 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.265 0.266 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.529 4.340
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.230 0.231 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.371 3.767
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.341 0.342 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.299 5.583
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.265 0.265 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.536 4.335
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.250 0.251 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.857 4.098
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.288 0.288 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.091 4.714
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1872 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.206 0.207 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.107 3.377
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.202 0.202 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.254 3.309
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.198 0.199 99.5
49: (ns/day) (hour/ns)
49: Performance: 7.384 3.250
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.206 0.206 99.7
49: (ns/day) (hour/ns)
49: Performance: 7.114 3.374
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.274 0.275 99.7
49: (ns/day) (hour/ns)
49: Performance: 5.348 4.487
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.244 0.245 99.6
49: (ns/day) (hour/ns)
49: Performance: 5.992 4.006
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1568 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.227 0.227 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.462 3.714
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.280 0.281 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.234 4.586
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.256 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.742 4.180
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.208 0.209 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.031 3.413
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.232 0.233 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.310 3.804
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.255 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.757 4.169
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1676 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.295 0.295 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.977 4.822
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.561 0.561 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.616 9.174
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.307 0.307 99.8
49: (ns/day) (hour/ns)
49: Performance: 4.780 5.020
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 1.077 1.077 100.0
49: (ns/day) (hour/ns)
49: Performance: 1.364 17.599
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.303 0.304 99.7
49: (ns/day) (hour/ns)
49: Performance: 4.839 4.960
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.248 0.248 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.914 4.058
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (3400 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.331 0.331 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.437 5.409
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.307 0.307 99.9
49: (ns/day) (hour/ns)
49: Performance: 4.779 5.022
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.240 0.241 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.095 3.937
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.230 0.231 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.371 3.767
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.533 0.533 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.756 8.709
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.293 0.294 99.6
49: (ns/day) (hour/ns)
49: Performance: 4.990 4.809
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (2150 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.239 0.239 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.139 3.910
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.209 0.209 99.7
49: (ns/day) (hour/ns)
49: Performance: 7.016 3.421
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.246 0.246 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.972 4.019
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.226 0.226 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.500 3.692
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.229 0.229 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.411 3.743
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49:
49: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Using Berendsen pressure coupling invalidates the true ensemble for the
49: thermostat
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49:
49: There was 1 warning
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.228 0.229 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.418 3.739
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1629 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.258 0.258 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.695 4.214
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.254 0.254 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.776 4.155
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.238 0.238 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.159 3.897
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.205 0.205 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.165 3.350
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.842 0.843 99.9
49: (ns/day) (hour/ns)
49: Performance: 1.743 13.769
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
49: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.229 0.230 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.393 3.754
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (2255 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.283 0.283 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.185 4.629
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.255 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.752 4.172
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.231 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.352 3.778
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.220 0.220 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.671 3.598
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.232 0.233 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.316 3.800
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.221 0.222 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.627 3.622
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1681 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.217 0.217 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.771 3.544
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.231 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.360 3.774
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.228 0.228 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.435 3.729
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.705 0.706 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.081 11.534
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.310 0.310 99.8
49: (ns/day) (hour/ns)
49: Performance: 4.734 5.070
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.231 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.348 3.780
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (2164 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.238 0.238 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.177 3.885
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.223 0.224 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.564 3.656
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.217 0.217 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.764 3.548
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.230 0.230 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.375 3.764
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.232 0.233 99.5
49: (ns/day) (hour/ns)
49: Performance: 6.311 3.803
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.280 0.281 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.233 4.587
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (1745 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.228 0.229 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.422 3.737
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.234 0.234 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.266 3.830
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.243 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.036 3.976
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.220 0.220 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.671 3.597
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.210 0.210 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.982 3.437
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.233 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.296 3.812
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1577 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.247 0.247 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.935 4.044
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.336 0.336 99.8
49: (ns/day) (hour/ns)
49: Performance: 4.370 5.493
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.775 0.775 99.9
49: (ns/day) (hour/ns)
49: Performance: 1.895 12.663
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.259 0.259 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.663 4.238
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.244 0.244 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.012 3.992
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
49: NVE simulation: will use the initial temperature of 68.810 K for
49: determining the Verlet buffer size
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.244 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.024 3.984
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (2320 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.585 0.585 100.0
49: (ns/day) (hour/ns)
49: Performance: 2.512 9.554
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.258 0.258 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.691 4.217
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.221 0.221 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.653 3.607
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.209 0.209 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.015 3.421
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.222 0.222 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.611 3.630
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.217 0.220 98.9
49: (ns/day) (hour/ns)
49: Performance: 6.691 3.587
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (1950 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.241 0.241 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.100 3.934
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.257 0.258 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.701 4.210
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.230 0.231 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.364 3.771
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.244 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.020 3.987
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.273 0.274 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.359 4.478
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.233 99.5
49: (ns/day) (hour/ns)
49: Performance: 6.313 3.802
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1695 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.249 0.250 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.886 4.077
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.226 0.226 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.496 3.694
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.248 0.248 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.921 4.053
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.194 0.194 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.568 3.171
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.218 0.219 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.715 3.574
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.229 0.230 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.391 3.755
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (1600 ms)
49: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.236 0.236 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.215 3.861
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.232 0.233 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.311 3.803
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.392 0.393 99.9
49: (ns/day) (hour/ns)
49: Performance: 3.739 6.419
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.660 0.660 99.9
49: (ns/day) (hour/ns)
49: Performance: 2.225 10.785
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.773 0.774 99.9
49: (ns/day) (hour/ns)
49: Performance: 1.898 12.643
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 1 of the 1 non-bonded parameter combinations
49: Excluding 1 bonded neighbours molecule type 'Argon'
49: Number of degrees of freedom in T-Coupling group System is 33.00
49:
49: There were 2 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'Argon'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
49: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.262 0.263 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.595 4.289
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
49: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (2789 ms)
49: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (35320 ms total)
49:
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.247 0.247 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.951 4.033
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.233 0.233 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.297 3.811
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.232 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.333 3.789
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: Non-default thread affinity set probably by the OpenMP library,
49: disabling internal thread affinity
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.256 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.744 4.179
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.196 0.196 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.479 3.209
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.268 0.268 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.477 4.382
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (26176 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.282 0.282 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.212 4.605
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.267 0.267 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.499 4.364
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.241 0.242 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.078 3.948
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.269 0.270 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.446 4.407
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.244 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.023 3.985
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.244 0.245 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.997 4.002
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (27730 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: Non-default thread affinity set probably by the OpenMP library,
49: disabling internal thread affinity
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.209 0.209 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.030 3.414
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.219 0.219 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.698 3.583
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: Non-default thread affinity set probably by the OpenMP library,
49: disabling internal thread affinity
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.247 0.247 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.938 4.042
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: Non-default thread affinity set probably by the OpenMP library,
49: disabling internal thread affinity
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.315 0.315 99.8
49: (ns/day) (hour/ns)
49: Performance: 4.659 5.151
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.254 0.255 99.8
49: (ns/day) (hour/ns)
49: Performance: 5.760 4.166
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.241 0.242 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.069 3.954
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (28513 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.205 0.206 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.137 3.363
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.226 0.226 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.489 3.699
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.235 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.247 3.842
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.230 0.230 99.7
49: (ns/day) (hour/ns)
49: Performance: 6.375 3.765
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.231 0.232 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.337 3.787
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.224 0.224 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.551 3.663
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (27580 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.255 0.255 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.750 4.174
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.207 0.207 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.100 3.380
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.212 0.212 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.919 3.469
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.206 0.206 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.128 3.367
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.195 0.195 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.519 3.192
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.202 0.202 99.8
49: (ns/day) (hour/ns)
49: Performance: 7.260 3.306
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (26199 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.286 0.286 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.138 4.672
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.263 0.263 99.9
49: (ns/day) (hour/ns)
49: Performance: 5.578 4.302
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.275 0.277 99.5
49: (ns/day) (hour/ns)
49: Performance: 5.310 4.520
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.241 0.241 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.084 3.945
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.240 0.240 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.121 3.921
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49: Using 1 OpenMP thread
49:
49:
49: Non-default thread affinity set probably by the OpenMP library,
49: disabling internal thread affinity
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.241 0.242 99.8
49: (ns/day) (hour/ns)
49: Performance: 6.076 3.950
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (28111 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.219 0.219 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.703 3.581
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.192 0.192 99.9
49: (ns/day) (hour/ns)
49: Performance: 7.663 3.132
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.216 0.216 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.794 3.532
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.236 0.236 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.223 3.857
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.236 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.236 3.849
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: NVE simulation: will use the initial temperature of 398.997 K for
49: determining the Verlet buffer size
49:
49:
49: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 4 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Can not increase nstlist because an NVE ensemble is used
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
49: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.243 0.243 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.050 3.967
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (27876 ms)
49: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.235 0.235 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.251 3.839
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.234 0.234 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.284 3.819
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.237 0.237 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.204 3.869
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.216 0.217 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.779 3.540
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.214 0.214 99.9
49: (ns/day) (hour/ns)
49: Performance: 6.868 3.495
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49:
49: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
49: that with the Verlet scheme, nstlist has no effect on the accuracy of
49: your simulation.
49:
49:
49: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: Setting nstcalcenergy (100) equal to nstenergy (4)
49:
49: Generated 330891 of the 330891 non-bonded parameter combinations
49: Generating 1-4 interactions: fudge = 0.5
49: Generated 330891 of the 330891 1-4 parameter combinations
49: Excluding 2 bonded neighbours molecule type 'SOL'
49: Number of degrees of freedom in T-Coupling group System is 27.00
49:
49: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
49: You are using a plain Coulomb cut-off, which might produce artifacts.
49: You might want to consider using PME electrostatics.
49:
49:
49:
49: There were 3 notes
49: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
49: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
49: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
49:
49: Using 1 MPI thread
49:
49: Non-default thread affinity set, disabling internal thread affinity
49:
49: Using 1 OpenMP thread
49:
49:
49: WARNING: Using the slow plain C kernels. This should
49: not happen during routine usage on supported platforms.
49: starting mdrun 'spc2'
49: 16 steps, 0.0 ps.
49: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
49: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
49: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
49: Note that mdrun will redetermine rlist based on the actual pair-list setup
49: This run will generate roughly 0 Mb of data
49:
49: Writing final coordinates.
49:
49: Core t (s) Wall t (s) (%)
49: Time: 0.403 0.403 100.0
49: (ns/day) (hour/ns)
49: Performance: 3.646 6.582
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
49: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
49: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (27814 ms)
49: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (220004 ms total)
49:
49: [----------] Global test environment tear-down
49: [==========] 27 tests from 3 test cases ran. (257186 ms total)
49: [ PASSED ] 27 tests.
49/54 Test #49: MdrunMpiCoordinationTestsOneRank .... Passed 257.28 sec
test 50
Start 50: MdrunMpiCoordinationTestsTwoRanks
50: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/mdrun-mpi-coordination-test "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/MdrunMpiCoordinationTestsTwoRanks.xml"
50: Test timeout computed to be: 960
50: [==========] Running 27 tests from 3 test cases.
50: [----------] Global test environment set-up.
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest
50: [ RUN ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.435 0.218 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.739 3.562
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.479 0.240 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.121 3.921
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.469 0.236 198.7
50: (ns/day) (hour/ns)
50: Performance: 6.224 3.856
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.447 0.225 198.7
50: (ns/day) (hour/ns)
50: Performance: 6.529 3.676
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.406 0.204 199.1
50: (ns/day) (hour/ns)
50: Performance: 7.206 3.330
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.408 0.205 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.168 3.348
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/BasicPropagators_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] BasicPropagators/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1613 ms)
50: [----------] 1 test from BasicPropagators/PeriodicActionsTest (1613 ms total)
50:
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.404 0.202 199.7
50: (ns/day) (hour/ns)
50: Performance: 7.260 3.306
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.436 0.218 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.729 3.567
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.473 0.237 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.198 3.872
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.471 0.236 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.219 3.859
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.433 0.217 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.775 3.542
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.496 0.249 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.906 4.063
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (1600 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.469 0.235 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.249 3.841
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.525 0.263 199.7
50: (ns/day) (hour/ns)
50: Performance: 5.584 4.298
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.516 0.258 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.683 4.223
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.513 0.257 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.713 4.201
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.428 0.215 198.9
50: (ns/day) (hour/ns)
50: Performance: 6.823 3.517
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.476 0.239 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.150 3.902
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (1716 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.448 0.224 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.553 3.662
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.460 0.231 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.369 3.768
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.493 0.248 199.3
50: (ns/day) (hour/ns)
50: Performance: 5.932 4.046
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.480 0.241 198.7
50: (ns/day) (hour/ns)
50: Performance: 6.085 3.944
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.555 0.279 198.9
50: (ns/day) (hour/ns)
50: Performance: 5.265 4.558
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.490 0.246 199.0
50: (ns/day) (hour/ns)
50: Performance: 5.969 4.021
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (1766 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.446 0.223 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.583 3.646
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.427 0.214 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.856 3.501
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.457 0.230 199.0
50: (ns/day) (hour/ns)
50: Performance: 6.395 3.753
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.462 0.232 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.338 3.787
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.432 0.217 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.772 3.544
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.398 0.199 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.363 3.260
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (1606 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.416 0.208 199.7
50: (ns/day) (hour/ns)
50: Performance: 7.056 3.401
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.468 0.234 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.264 3.831
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.507 0.254 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.782 4.151
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.517 0.260 199.0
50: (ns/day) (hour/ns)
50: Performance: 5.658 4.242
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.473 0.238 198.9
50: (ns/day) (hour/ns)
50: Performance: 6.175 3.886
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.496 0.249 199.0
50: (ns/day) (hour/ns)
50: Performance: 5.895 4.071
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (1743 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.446 0.223 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.576 3.649
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.488 0.245 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.002 3.998
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.452 0.227 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.482 3.703
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.428 0.215 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.844 3.507
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.413 0.207 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.101 3.380
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.367 0.684 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.147 11.177
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (2042 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.231 0.616 199.9
50: (ns/day) (hour/ns)
50: Performance: 2.384 10.067
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.575 0.288 199.7
50: (ns/day) (hour/ns)
50: Performance: 5.102 4.704
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.197 0.599 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.451 9.794
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.588 0.295 199.6
50: (ns/day) (hour/ns)
50: Performance: 4.984 4.815
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.547 0.774 199.8
50: (ns/day) (hour/ns)
50: Performance: 1.897 12.653
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.211 0.606 199.7
50: (ns/day) (hour/ns)
50: Performance: 2.422 9.908
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (3412 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.520 0.260 199.7
50: (ns/day) (hour/ns)
50: Performance: 5.640 4.256
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.431 0.216 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.796 3.531
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.415 0.208 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.051 3.404
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.436 0.219 198.9
50: (ns/day) (hour/ns)
50: Performance: 6.692 3.586
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.418 0.210 199.0
50: (ns/day) (hour/ns)
50: Performance: 6.993 3.432
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50:
50: WARNING 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Using Berendsen pressure coupling invalidates the true ensemble for the
50: thermostat
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50:
50: There was 1 warning
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.449 0.225 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.526 3.677
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (1627 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.536 0.268 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.475 4.384
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.471 0.236 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.222 3.857
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.599 0.300 199.6
50: (ns/day) (hour/ns)
50: Performance: 4.897 4.901
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.514 0.257 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.705 4.207
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.518 0.259 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.664 4.238
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_input.mdp]:
50: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.525 0.263 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.586 4.296
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_8.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/8 (1851 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.404 0.202 199.7
50: (ns/day) (hour/ns)
50: Performance: 7.262 3.305
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.390 0.196 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.505 3.198
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.485 0.243 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.044 3.971
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.456 0.229 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.415 3.741
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.511 0.256 199.4
50: (ns/day) (hour/ns)
50: Performance: 5.732 4.187
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.490 0.246 199.1
50: (ns/day) (hour/ns)
50: Performance: 5.964 4.024
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_9.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/9 (1622 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.514 0.258 199.7
50: (ns/day) (hour/ns)
50: Performance: 5.702 4.209
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.571 0.286 199.7
50: (ns/day) (hour/ns)
50: Performance: 5.133 4.676
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.475 0.238 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.174 3.887
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.433 0.217 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.759 3.551
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.445 0.223 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.580 3.647
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.561 0.281 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.229 4.590
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_10.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/10 (1789 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.114 0.557 199.9
50: (ns/day) (hour/ns)
50: Performance: 2.636 9.106
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.652 0.326 199.6
50: (ns/day) (hour/ns)
50: Performance: 4.500 5.334
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.511 0.256 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.729 4.189
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.491 0.246 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.966 4.023
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.530 0.265 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.535 4.336
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.430 0.216 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.812 3.523
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_11.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/11 (2133 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.400 0.201 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.318 3.280
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.366 0.184 199.1
50: (ns/day) (hour/ns)
50: Performance: 7.988 3.005
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.455 0.228 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.433 3.731
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.420 0.212 198.4
50: (ns/day) (hour/ns)
50: Performance: 6.935 3.461
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.377 0.190 199.0
50: (ns/day) (hour/ns)
50: Performance: 7.748 3.098
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.405 0.204 199.0
50: (ns/day) (hour/ns)
50: Performance: 7.215 3.327
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_12.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/12 (1490 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.490 0.245 199.7
50: (ns/day) (hour/ns)
50: Performance: 5.986 4.009
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.385 0.693 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.120 11.322
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.494 0.248 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.930 4.047
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.447 0.224 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.552 3.663
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.475 0.238 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.174 3.887
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_input.mdp]:
50: NVE simulation: will use the initial temperature of 68.810 K for
50: determining the Verlet buffer size
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 68.8096 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.447 0.224 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.551 3.664
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_13.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/13 (2120 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.397 0.199 199.3
50: (ns/day) (hour/ns)
50: Performance: 7.367 3.258
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.394 0.198 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.420 3.235
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.519 0.260 199.3
50: (ns/day) (hour/ns)
50: Performance: 5.645 4.251
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.494 0.748 199.8
50: (ns/day) (hour/ns)
50: Performance: 1.964 12.220
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.456 0.729 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.015 11.910
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.309 0.655 199.7
50: (ns/day) (hour/ns)
50: Performance: 2.242 10.706
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_14.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/14 (3102 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.443 0.222 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.612 3.630
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.525 0.263 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.585 4.297
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.471 0.236 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.216 3.861
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.521 0.261 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.631 4.262
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.489 0.247 198.1
50: (ns/day) (hour/ns)
50: Performance: 5.948 4.035
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.454 0.228 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.445 3.724
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_15.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/15 (1721 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.400 0.200 199.5
50: (ns/day) (hour/ns)
50: Performance: 7.328 3.275
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.367 0.187 196.2
50: (ns/day) (hour/ns)
50: Performance: 7.845 3.059
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.438 0.220 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.691 3.587
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.083 0.542 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.709 8.860
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 1.184 0.593 199.8
50: (ns/day) (hour/ns)
50: Performance: 2.478 9.684
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.510 0.256 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.742 4.179
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_16.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/16 (2289 ms)
50: [ RUN ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.462 0.231 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.350 3.779
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.519 0.260 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.646 4.251
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.487 0.244 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.019 3.987
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.454 0.228 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.454 3.719
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.459 0.230 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.390 3.756
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 1 of the 1 non-bonded parameter combinations
50: Excluding 1 bonded neighbours molecule type 'Argon'
50: Number of degrees of freedom in T-Coupling group System is 33.00
50:
50: There were 2 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 100, rlist from 0.701 to 0.734
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'Argon'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 80 K
50: Calculated rlist for 1x1 atom pair-list as 0.701 nm, buffer size 0.001 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.701 nm, buffer size 0.001 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.592 0.296 199.6
50: (ns/day) (hour/ns)
50: Performance: 4.955 4.844
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithCoupling_PeriodicActionsTest_PeriodicActionsAgreeWithReference_17.edr as double precision energy file
50: [ OK ] PropagatorsWithCoupling/PeriodicActionsTest.PeriodicActionsAgreeWithReference/17 (1731 ms)
50: [----------] 18 tests from PropagatorsWithCoupling/PeriodicActionsTest (35363 ms total)
50:
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.404 0.202 199.6
50: (ns/day) (hour/ns)
50: Performance: 7.264 3.304
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.412 0.207 199.5
50: (ns/day) (hour/ns)
50: Performance: 7.107 3.377
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.469 0.235 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.244 3.844
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.474 0.238 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.180 3.884
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.483 0.242 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.067 3.956
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.577 0.289 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.080 4.724
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_0.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/0 (26523 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.480 0.241 199.7
50: (ns/day) (hour/ns)
50: Performance: 6.106 3.931
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.550 0.275 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.334 4.500
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.576 0.288 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.094 4.712
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.537 0.269 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.462 4.394
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.458 0.230 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.394 3.754
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.525 0.264 199.1
50: (ns/day) (hour/ns)
50: Performance: 5.572 4.307
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_1.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/1 (28052 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.427 0.214 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.870 3.494
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.428 0.215 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.841 3.508
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.426 0.214 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.871 3.493
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.407 0.205 198.7
50: (ns/day) (hour/ns)
50: Performance: 7.172 3.346
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.495 0.249 199.3
50: (ns/day) (hour/ns)
50: Performance: 5.910 4.061
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.501 0.251 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.844 4.107
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_2.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/2 (27470 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.512 0.257 199.6
50: (ns/day) (hour/ns)
50: Performance: 5.723 4.193
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.466 0.234 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.283 3.820
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.472 0.237 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.205 3.868
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.471 0.236 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.220 3.859
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.493 0.247 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.948 4.035
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.418 0.209 199.4
50: (ns/day) (hour/ns)
50: Performance: 7.015 3.421
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_3.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/3 (28469 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.452 0.227 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.480 3.704
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.474 0.238 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.180 3.884
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.553 0.277 199.5
50: (ns/day) (hour/ns)
50: Performance: 5.301 4.527
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.441 0.222 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.631 3.619
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.451 0.226 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.487 3.700
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.443 0.222 199.5
50: (ns/day) (hour/ns)
50: Performance: 6.609 3.631
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_4.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/4 (28989 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.457 0.229 199.6
50: (ns/day) (hour/ns)
50: Performance: 6.416 3.741
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.480 0.243 198.0
50: (ns/day) (hour/ns)
50: Performance: 6.055 3.964
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.448 0.224 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.544 3.668
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.472 0.237 199.4
50: (ns/day) (hour/ns)
50: Performance: 6.209 3.865
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.552 0.278 198.9
50: (ns/day) (hour/ns)
50: Performance: 5.288 4.539
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.523 0.263 199.0
50: (ns/day) (hour/ns)
50: Performance: 5.586 4.296
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_5.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/5 (28203 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.407 0.204 199.2
50: (ns/day) (hour/ns)
50: Performance: 7.197 3.335
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.449 0.225 199.3
50: (ns/day) (hour/ns)
50: Performance: 6.521 3.681
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.461 0.232 199.2
50: (ns/day) (hour/ns)
50: Performance: 6.343 3.784
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.552 0.277 199.3
50: (ns/day) (hour/ns)
50: Performance: 5.309 4.521
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.449 0.227 197.8
50: (ns/day) (hour/ns)
50: Performance: 6.468 3.710
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: NVE simulation: will use the initial temperature of 398.997 K for
50: determining the Verlet buffer size
50:
50:
50: NOTE 4 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 4 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Can not increase nstlist because an NVE ensemble is used
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 398.997 K
50: Calculated rlist for 1x1 atom pair-list as 0.774 nm, buffer size 0.074 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.769 nm, buffer size 0.069 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.425 0.213 199.1
50: (ns/day) (hour/ns)
50: Performance: 6.880 3.488
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_6.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/6 (28358 ms)
50: [ RUN ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.467 0.236 197.5
50: (ns/day) (hour/ns)
50: Performance: 6.216 3.861
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.561 0.282 199.3
50: (ns/day) (hour/ns)
50: Performance: 5.216 4.601
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.537 0.269 199.3
50: (ns/day) (hour/ns)
50: Performance: 5.454 4.401
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
Reading energy frame 0 time 0.000
Reading energy frame 0 time 0.000
Reading energy frame 1 time 0.004
Reading energy frame 1 time 0.004
Reading energy frame 2 time 0.008
Reading energy frame 2 time 0.008
Reading energy frame 3 time 0.012
Reading energy frame 3 time 0.012
Reading energy frame 4 time 0.016
Reading energy frame 4 time 0.016
Last energy frame read 4 time 0.016
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.457 0.230 199.1
50: (ns/day) (hour/ns)
50: Performance: 6.399 3.750
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.493 0.248 198.8
50: (ns/day) (hour/ns)
50: Performance: 5.922 4.053
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50:
50: NOTE 1 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
50: that with the Verlet scheme, nstlist has no effect on the accuracy of
50: your simulation.
50:
50:
50: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: Setting nstcalcenergy (100) equal to nstenergy (4)
50:
50: Generated 330891 of the 330891 non-bonded parameter combinations
50: Generating 1-4 interactions: fudge = 0.5
50: Generated 330891 of the 330891 1-4 parameter combinations
50: Excluding 2 bonded neighbours molecule type 'SOL'
50: Number of degrees of freedom in T-Coupling group System is 27.00
50:
50: NOTE 3 [file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_input.mdp]:
50: You are using a plain Coulomb cut-off, which might produce artifacts.
50: You might want to consider using PME electrostatics.
50:
50:
50:
50: There were 3 notes
50: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
50: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
50: Changing nstlist from 8 to 25, rlist from 0.759 to 0.912
50:
50: Using 2 MPI threads
50: Using 1 OpenMP thread per tMPI thread
50:
50:
50: NOTE: The number of threads is not equal to the number of (logical) cores
50: and the -pin option is set to auto: will not pin threads to cores.
50: This can lead to significant performance degradation.
50: Consider using -pin on (and -pinoffset in case you run multiple jobs).
50:
50: WARNING: Using the slow plain C kernels. This should
50: not happen during routine usage on supported platforms.
50: starting mdrun 'spc2'
50: 16 steps, 0.0 ps.
50: Determining Verlet buffer for a tolerance of 1e-06 kJ/mol/ps at 298 K
50: Calculated rlist for 1x1 atom pair-list as 0.763 nm, buffer size 0.063 nm
50: Set rlist, assuming 4x4 atom pair-list, to 0.759 nm, buffer size 0.059 nm
50: Note that mdrun will redetermine rlist based on the actual pair-list setup
50: This run will generate roughly 0 Mb of data
50:
50: Writing final coordinates.
50:
50: Core t (s) Wall t (s) (%)
50: Time: 0.472 0.237 199.0
50: (ns/day) (hour/ns)
50: Performance: 6.191 3.877
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7_reference.edr as double precision energy file
50: Opened /<<PKGBUILDDIR>>/build/basic-dp/src/programs/mdrun/tests/Testing/Temporary/PropagatorsWithConstraints_PeriodicActionsTest_PeriodicActionsAgreeWithReference_7.edr as double precision energy file
50: [ OK ] PropagatorsWithConstraints/PeriodicActionsTest.PeriodicActionsAgreeWithReference/7 (28121 ms)
50: [----------] 8 tests from PropagatorsWithConstraints/PeriodicActionsTest (224189 ms total)
50:
50: [----------] Global test environment tear-down
50: [==========] 27 tests from 3 test cases ran. (261168 ms total)
50: [ PASSED ] 27 tests.
50/54 Test #50: MdrunMpiCoordinationTestsTwoRanks ... Passed 261.26 sec
test 51
Start 51: GmxapiExternalInterfaceTests
51: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiExternalInterfaceTests.xml"
51: Test timeout computed to be: 600
51: [==========] Running 9 tests from 2 test cases.
51: [----------] Global test environment set-up.
51: [----------] 8 tests from GmxApiTest
51: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
51: Setting the LD random seed to 1878783987
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.537 0.269 199.8
51: (ns/day) (hour/ns)
51: Performance: 1.882 12.749
51: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (4416 ms)
51: [ RUN ] GmxApiTest.SystemConstruction
51: Setting the LD random seed to -874848590
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51: [ OK ] GmxApiTest.SystemConstruction (4399 ms)
51: [ RUN ] GmxApiTest.SaneVersionComparisons
51: [ OK ] GmxApiTest.SaneVersionComparisons (0 ms)
51: [ RUN ] GmxApiTest.VersionNamed0_1_Features
51: [ OK ] GmxApiTest.VersionNamed0_1_Features (1 ms)
51: [ RUN ] GmxApiTest.RunnerBasicMD
51: Setting the LD random seed to -2402369
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 1.052 0.526 199.9
51: (ns/day) (hour/ns)
51: Performance: 0.962 24.948
51: [ OK ] GmxApiTest.RunnerBasicMD (5033 ms)
51: [ RUN ] GmxApiTest.RunnerReinitialize
51: Setting the LD random seed to -271270929
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51:
51: Received the remote INT/TERM signal, stopping within 50 steps
51:
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.565 0.283 199.7
51: (ns/day) (hour/ns)
51: Performance: 12.512 1.918
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.518 0.260 199.4
51: (ns/day) (hour/ns)
51: Performance: 13.639 1.760
51: [ OK ] GmxApiTest.RunnerReinitialize (4656 ms)
51: [ RUN ] GmxApiTest.RunnerContinuedMD
51: Setting the LD random seed to -1082130465
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 10 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.651 0.326 199.7
51: (ns/day) (hour/ns)
51: Performance: 5.695 4.214
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
51: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
51: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
51:
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 20 steps, 0.0 ps.
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.541 0.271 199.4
51: (ns/day) (hour/ns)
51: Performance: 13.067 1.837
51: [ OK ] GmxApiTest.RunnerContinuedMD (5033 ms)
51: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
51: Setting the LD random seed to 1589497849
51: Generated 331705 of the 331705 non-bonded parameter combinations
51: Generating 1-4 interactions: fudge = 0.5
51: Generated 331705 of the 331705 1-4 parameter combinations
51: Excluding 2 bonded neighbours molecule type 'SOL'
51: Excluding 3 bonded neighbours molecule type 'methane'
51:
51: NOTE 1 [file spc_and_methane.top, line 33]:
51: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
51: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
51: the time step of 2.0e-03 ps.
51: Maybe you forgot to change the constraints mdp option.
51:
51: Number of degrees of freedom in T-Coupling group System is 18.00
51:
51: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
51: You are using a plain Coulomb cut-off, which might produce artifacts.
51: You might want to consider using PME electrostatics.
51:
51:
51:
51: There were 2 notes
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 1 steps, 0.0 ps.
51: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
51: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
51: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
51: Note that mdrun will redetermine rlist based on the actual pair-list setup
51: This run will generate roughly 0 Mb of data
51:
51: Writing final coordinates.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.499 0.250 199.8
51: (ns/day) (hour/ns)
51: Performance: 1.351 17.760
51: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
51: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
51: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
51: Changing nstlist from 10 to 1, rlist from 1.041 to 1
51:
51:
51: Using 1 MPI thread
51: Using 2 OpenMP threads
51:
51:
51: NOTE: The number of threads is not equal to the number of (logical) cores
51: and the -pin option is set to auto: will not pin threads to cores.
51: This can lead to significant performance degradation.
51: Consider using -pin on (and -pinoffset in case you run multiple jobs).
51:
51: WARNING: Using the slow plain C kernels. This should
51: not happen during routine usage on supported platforms.
51: starting mdrun 'Water and methane'
51: 2 steps, 0.0 ps.
51:
51: Core t (s) Wall t (s) (%)
51: Time: 0.477 0.239 199.5
51: (ns/day) (hour/ns)
51: Performance: 1.412 17.002
51: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (4611 ms)
51: [----------] 8 tests from GmxApiTest (28151 ms total)
51:
51: [----------] 1 test from GmxApiBasicTest
51: [ RUN ] GmxApiBasicTest.Status
51: [ OK ] GmxApiBasicTest.Status (0 ms)
51: [----------] 1 test from GmxApiBasicTest (1 ms total)
51:
51: [----------] Global test environment tear-down
51: [==========] 9 tests from 2 test cases ran. (28153 ms total)
51: [ PASSED ] 9 tests.
51/54 Test #51: GmxapiExternalInterfaceTests ........ Passed 28.25 sec
test 52
Start 52: GmxapiMpiTests
52: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/gmxapi-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiMpiTests.xml"
52: Test timeout computed to be: 600
52: [==========] Running 9 tests from 2 test cases.
52: [----------] Global test environment set-up.
52: [----------] 8 tests from GmxApiTest
52: [ RUN ] GmxApiTest.ApiRunnerRestrainedMD
52: Setting the LD random seed to -1816737601
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.681 0.341 199.8
52: (ns/day) (hour/ns)
52: Performance: 1.486 16.153
52: [ OK ] GmxApiTest.ApiRunnerRestrainedMD (4775 ms)
52: [ RUN ] GmxApiTest.SystemConstruction
52: Setting the LD random seed to -537200772
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_SystemConstruction_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52: [ OK ] GmxApiTest.SystemConstruction (4415 ms)
52: [ RUN ] GmxApiTest.SaneVersionComparisons
52: [ OK ] GmxApiTest.SaneVersionComparisons (1 ms)
52: [ RUN ] GmxApiTest.VersionNamed0_1_Features
52: [ OK ] GmxApiTest.VersionNamed0_1_Features (0 ms)
52: [ RUN ] GmxApiTest.RunnerBasicMD
52: Setting the LD random seed to 855569847
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerBasicMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.468 0.234 199.7
52: (ns/day) (hour/ns)
52: Performance: 2.163 11.098
52: [ OK ] GmxApiTest.RunnerBasicMD (4733 ms)
52: [ RUN ] GmxApiTest.RunnerReinitialize
52: Setting the LD random seed to -1770915139
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52:
52: Received the remote INT/TERM signal, stopping within 50 steps
52:
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.577 0.289 199.7
52: (ns/day) (hour/ns)
52: Performance: 12.264 1.957
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerReinitialize.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.542 0.272 199.2
52: (ns/day) (hour/ns)
52: Performance: 13.029 1.842
52: [ OK ] GmxApiTest.RunnerReinitialize (4993 ms)
52: [ RUN ] GmxApiTest.RunnerContinuedMD
52: Setting the LD random seed to -1367634092
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 10 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.646 0.324 199.7
52: (ns/day) (hour/ns)
52: Performance: 5.736 4.184
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_RunnerContinuedMD.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
52: Overriding nsteps with value passed on the command line: 20 steps, 0.0391 ps
52: Changing nstlist from 10 to 50, rlist from 1.041 to 1.296
52:
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 20 steps, 0.0 ps.
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.509 0.255 199.2
52: (ns/day) (hour/ns)
52: Performance: 13.877 1.729
52: [ OK ] GmxApiTest.RunnerContinuedMD (5010 ms)
52: [ RUN ] GmxApiTest.ApiRunnerStopSignalClient
52: Setting the LD random seed to -1073762313
52: Generated 331705 of the 331705 non-bonded parameter combinations
52: Generating 1-4 interactions: fudge = 0.5
52: Generated 331705 of the 331705 1-4 parameter combinations
52: Excluding 2 bonded neighbours molecule type 'SOL'
52: Excluding 3 bonded neighbours molecule type 'methane'
52:
52: NOTE 1 [file spc_and_methane.top, line 33]:
52: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
52: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
52: the time step of 2.0e-03 ps.
52: Maybe you forgot to change the constraints mdp option.
52:
52: Number of degrees of freedom in T-Coupling group System is 18.00
52:
52: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient_input.mdp]:
52: You are using a plain Coulomb cut-off, which might produce artifacts.
52: You might want to consider using PME electrostatics.
52:
52:
52:
52: There were 2 notes
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 1 steps, 0.0 ps.
52: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
52: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
52: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
52: Note that mdrun will redetermine rlist based on the actual pair-list setup
52: This run will generate roughly 0 Mb of data
52:
52: Writing final coordinates.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.585 0.293 199.8
52: (ns/day) (hour/ns)
52: Performance: 1.153 20.814
52: Compiled SIMD: None, but for this host/run ARM_NEON might be better (see log).
52: Reading file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerStopSignalClient.tpr, VERSION 2020.6-Raspbian-2020.6-2 (double precision)
52: Overriding nsteps with value passed on the command line: 2 steps, 0.00391 ps
52: Changing nstlist from 10 to 1, rlist from 1.041 to 1
52:
52:
52: Using 1 MPI thread
52:
52: Non-default thread affinity set, disabling internal thread affinity
52:
52: Using 2 OpenMP threads
52:
52:
52: WARNING: Using the slow plain C kernels. This should
52: not happen during routine usage on supported platforms.
52: starting mdrun 'Water and methane'
52: 2 steps, 0.0 ps.
52:
52: Core t (s) Wall t (s) (%)
52: Time: 0.475 0.238 199.6
52: (ns/day) (hour/ns)
52: Performance: 1.417 16.937
52: [ OK ] GmxApiTest.ApiRunnerStopSignalClient (5039 ms)
52: [----------] 8 tests from GmxApiTest (28968 ms total)
52:
52: [----------] 1 test from GmxApiBasicTest
52: [ RUN ] GmxApiBasicTest.Status
52: [ OK ] GmxApiBasicTest.Status (0 ms)
52: [----------] 1 test from GmxApiBasicTest (0 ms total)
52:
52: [----------] Global test environment tear-down
52: [==========] 9 tests from 2 test cases ran. (28969 ms total)
52: [ PASSED ] 9 tests.
52/54 Test #52: GmxapiMpiTests ...................... Passed 29.07 sec
test 53
Start 53: GmxapiInternalInterfaceTests
53: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-test "-ntomp" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalInterfaceTests.xml"
53: Test timeout computed to be: 600
53: [==========] Running 2 tests from 1 test case.
53: [----------] Global test environment set-up.
53: [----------] 2 tests from GmxApiTest
53: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
53: Setting the LD random seed to 2103164799
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.BuildApiWorkflowImpl (4273 ms)
53: [ RUN ] GmxApiTest.CreateApiWorkflow
53: Setting the LD random seed to -1914912807
53: Generated 331705 of the 331705 non-bonded parameter combinations
53: Generating 1-4 interactions: fudge = 0.5
53: Generated 331705 of the 331705 1-4 parameter combinations
53: Excluding 2 bonded neighbours molecule type 'SOL'
53: Excluding 3 bonded neighbours molecule type 'methane'
53:
53: NOTE 1 [file spc_and_methane.top, line 33]:
53: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
53: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
53: the time step of 2.0e-03 ps.
53: Maybe you forgot to change the constraints mdp option.
53:
53: Number of degrees of freedom in T-Coupling group System is 18.00
53:
53: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
53: You are using a plain Coulomb cut-off, which might produce artifacts.
53: You might want to consider using PME electrostatics.
53:
53:
53:
53: There were 2 notes
53: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
53: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
53: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
53: Note that mdrun will redetermine rlist based on the actual pair-list setup
53: This run will generate roughly 0 Mb of data
53: [ OK ] GmxApiTest.CreateApiWorkflow (4415 ms)
53: [----------] 2 tests from GmxApiTest (8690 ms total)
53:
53: [----------] Global test environment tear-down
53: [==========] 2 tests from 1 test case ran. (8691 ms total)
53: [ PASSED ] 2 tests.
53/54 Test #53: GmxapiInternalInterfaceTests ........ Passed 8.77 sec
test 54
Start 54: GmxapiInternalsMpiTests
54: Test command: /<<PKGBUILDDIR>>/build/basic-dp/bin/workflow-details-mpi-test "-ntomp" "2" "-ntmpi" "2" "--gtest_output=xml:/<<PKGBUILDDIR>>/build/basic-dp/Testing/Temporary/GmxapiInternalsMpiTests.xml"
54: Test timeout computed to be: 600
54: [==========] Running 2 tests from 1 test case.
54: [----------] Global test environment set-up.
54: [----------] 2 tests from GmxApiTest
54: [ RUN ] GmxApiTest.BuildApiWorkflowImpl
54: Setting the LD random seed to -365169297
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.BuildApiWorkflowImpl (4009 ms)
54: [ RUN ] GmxApiTest.CreateApiWorkflow
54: Setting the LD random seed to 2138869718
54: Generated 331705 of the 331705 non-bonded parameter combinations
54: Generating 1-4 interactions: fudge = 0.5
54: Generated 331705 of the 331705 1-4 parameter combinations
54: Excluding 2 bonded neighbours molecule type 'SOL'
54: Excluding 3 bonded neighbours molecule type 'methane'
54:
54: NOTE 1 [file spc_and_methane.top, line 33]:
54: The bond in molecule-type methane between atoms 1 C and 2 H1 has an
54: estimated oscillational period of 1.1e-02 ps, which is less than 10 times
54: the time step of 2.0e-03 ps.
54: Maybe you forgot to change the constraints mdp option.
54:
54: Number of degrees of freedom in T-Coupling group System is 18.00
54:
54: NOTE 2 [file /<<PKGBUILDDIR>>/build/basic-dp/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_CreateApiWorkflow_input.mdp]:
54: You are using a plain Coulomb cut-off, which might produce artifacts.
54: You might want to consider using PME electrostatics.
54:
54:
54:
54: There were 2 notes
54: Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
54: Calculated rlist for 1x1 atom pair-list as 1.041 nm, buffer size 0.041 nm
54: Set rlist, assuming 4x4 atom pair-list, to 1.041 nm, buffer size 0.041 nm
54: Note that mdrun will redetermine rlist based on the actual pair-list setup
54: This run will generate roughly 0 Mb of data
54: [ OK ] GmxApiTest.CreateApiWorkflow (4214 ms)
54: [----------] 2 tests from GmxApiTest (8224 ms total)
54:
54: [----------] Global test environment tear-down
54: [==========] 2 tests from 1 test case ran. (8225 ms total)
54: [ PASSED ] 2 tests.
54/54 Test #54: GmxapiInternalsMpiTests ............. Passed 8.31 sec
100% tests passed, 0 tests failed out of 54
Label Time Summary:
GTest = 949.42 sec*proc (54 tests)
IntegrationTest = 351.86 sec*proc (12 tests)
MpiTest = 629.73 sec*proc (8 tests)
SlowTest = 518.54 sec*proc (2 tests)
UnitTest = 79.02 sec*proc (40 tests)
Total Test time (real) = 949.85 sec
touch build-basic
dh_testdir
/usr/bin/make -j4 -C build/mpich
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/mpich --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich/CMakeFiles /<<PKGBUILDDIR>>/build/mpich//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Raspbian-2020.6-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/mpich/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.6-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
Scanning dependencies of target scanner
Scanning dependencies of target thread_mpi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
[ 0%] Built target release-version-info
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 1%] Built target thread_mpi
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 1%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 1%] Built target scanner
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/programs /<<PKGBUILDDIR>>/build/mpich/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
[ 1%] Built target linearalgebra
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=0 -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 5%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[ 8%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/gromacs /<<PKGBUILDDIR>>/build/mpich/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<float, float>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<float, float>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2293 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<float> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/multisim.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/printtime.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/threadaffinity.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state_propagator_data_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/abstractsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/behaviorcollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/filenameoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/options.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/options.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsassigner.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/optionsvisitor.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/timeunitmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/options/treesupport.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/manager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/restraint/restraintmdmodule.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual void gmx::DoubleOptionStorage::processSetValues(gmx::OptionStorageTemplate<double>::ValueList*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidegpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/decidesimulationworkload.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/findallgputasks.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/reportgpuusage.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/resourcedivision.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double, std::allocator<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/taskassignment.cpp
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = double]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, std::allocator<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const long long int&}; _Tp = long long int; _Alloc = std::allocator<long long int>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<long long int, std::allocator<long long int> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/options/basicoptions.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionStorageTemplate<T>::addValue(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreVector<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::OptionValueStoreNull<T>::append(const T&) [with T = long long int]':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<long long int*, std::vector<long long int, std::allocator<long long int> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/taskassignment/usergpuids.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/energyframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/trajectory/trajectoryframe.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mimic/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o -c /<<PKGBUILDDIR>>/build/mpich/src/gromacs/utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/checkpoint.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/confio.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mimic/communicator.cpp:37:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::BasicVector<float> >, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/enxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/espio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/filetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/g96io.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmx_internal_xdr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio_xdr.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/gmxfio.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {}; _Tp = gmx_file_position_t; _Alloc = std::allocator<gmx_file_position_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx_file_position_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<gmx_file_position_t> gmx_fio_get_output_file_positions()':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx_file_position_t*, std::vector<gmx_file_position_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/groio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/libxdrf.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/md5.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymap.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcdensitymapheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mrcserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/mtxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/oenv.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/pdbio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/readinp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/timecontrol.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tngio.cpp
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp: In function 't_matelmt searchcmap(gmx::ArrayRef<const t_mapping>, t_xpmelmt)':
/<<PKGBUILDDIR>>/src/gromacs/fileio/matio.cpp:114:11: note: parameter passing for argument of type 'gmx::ArrayRef<const t_mapping>' changed in GCC 7.1
114 | t_matelmt searchcmap(ArrayRef<const t_mapping> map, t_xpmelmt c)
| ^~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/tpxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trrio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/trxio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/vmdio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/warninp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xdrd.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/fileio/writeps.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_rgb}; _Tp = t_rgb; _Alloc = std::allocator<t_rgb>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<t_rgb>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'gmx::index search_col(t_psdata*, real, real, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<t_rgb*, std::vector<t_rgb> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xtcio.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fileio/xvgr.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/centerofmass.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/compiler.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/evaluate.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/indexutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/mempool.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/nbsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/params.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parsetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/poscalc.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/position.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectioncollection.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoption.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionbehavior.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selectionoptionmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selelem.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selhelp.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selmethod.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/selvalue.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_distance.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_insolidangle.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_keywords.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_merge.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_permute.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_position.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_same.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/sm_simple.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/symrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -P CMakeFiles/libgromacs.dir/cmake_clean_target.cmake
cd /<<PKGBUILDDIR>>/build/mpich/src/gromacs && /usr/bin/cmake -E cmake_link_script CMakeFiles/libgromacs.dir/link.txt --verbose=1
/usr/bin/ar qc ../../lib/libgromacs_mdrun_mpi.mpich.a CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o CMakeFiles/libgromacs.dir/utility/any.cpp.o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o CMakeFiles/libgromacs.dir/utility/compare.cpp.o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o CMakeFiles/libgromacs.dir/utility/futil.cpp.o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o CMakeFiles/libgromacs.dir/utility/init.cpp.o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o CMakeFiles/libgromacs.dir/utility/logger.cpp.o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o CMakeFiles/libgromacs.dir/utility/path.cpp.o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o CMakeFiles/libgromacs.dir/domdec/box.cpp.o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o CMakeFiles/libgromacs.dir/math/functions.cpp.o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o CMakeFiles/libgromacs.dir/math/units.cpp.o CMakeFiles/libgromacs.dir/math/utilities.cpp.o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o CMakeFiles/libgromacs.dir/random/seed.cpp.o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o CMakeFiles/libgromacs.dir/topology/block.cpp.o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o CMakeFiles/libgromacs.dir/topology/idef.cpp.o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o CMakeFiles/libgromacs.dir/topology/index.cpp.o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o CMakeFiles/libgromacs.dir/topology/topology.cpp.o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o CMakeFiles/libgromacs.dir/pulling/output.cpp.o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o CMakeFiles/libgromacs.dir/awh/awh.cpp.o CMakeFiles/libgromacs.dir/awh/bias.cpp.o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o CMakeFiles/libgromacs.dir/awh/grid.cpp.o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o CMakeFiles/libgromacs.dir/simd/support.cpp.o CMakeFiles/libgromacs.dir/imd/imd.cpp.o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o CMakeFiles/libgromacs.dir/fft/fft.cpp.o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/multisim.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/printtime.cpp.o CMakeFiles/libgromacs.dir/mdrunutility/threadaffinity.cpp.o CMakeFiles/libgromacs.dir/mdtypes/state_propagator_data_gpu_impl.cpp.o CMakeFiles/libgromacs.dir/options/abstractoption.cpp.o CMakeFiles/libgromacs.dir/options/abstractsection.cpp.o CMakeFiles/libgromacs.dir/options/basicoptions.cpp.o CMakeFiles/libgromacs.dir/options/behaviorcollection.cpp.o CMakeFiles/libgromacs.dir/options/filenameoption.cpp.o CMakeFiles/libgromacs.dir/options/filenameoptionmanager.cpp.o CMakeFiles/libgromacs.dir/options/options.cpp.o CMakeFiles/libgromacs.dir/options/optionsassigner.cpp.o CMakeFiles/libgromacs.dir/options/optionsection.cpp.o CMakeFiles/libgromacs.dir/options/optionsvisitor.cpp.o CMakeFiles/libgromacs.dir/options/timeunitmanager.cpp.o CMakeFiles/libgromacs.dir/options/treesupport.cpp.o CMakeFiles/libgromacs.dir/restraint/manager.cpp.o CMakeFiles/libgromacs.dir/restraint/restraintmdmodule.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidegpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/decidesimulationworkload.cpp.o CMakeFiles/libgromacs.dir/taskassignment/findallgputasks.cpp.o CMakeFiles/libgromacs.dir/taskassignment/reportgpuusage.cpp.o CMakeFiles/libgromacs.dir/taskassignment/resourcedivision.cpp.o CMakeFiles/libgromacs.dir/taskassignment/taskassignment.cpp.o CMakeFiles/libgromacs.dir/taskassignment/usergpuids.cpp.o CMakeFiles/libgromacs.dir/trajectory/energyframe.cpp.o CMakeFiles/libgromacs.dir/trajectory/trajectoryframe.cpp.o CMakeFiles/libgromacs.dir/mimic/communicator.cpp.o CMakeFiles/libgromacs.dir/mimic/utilities.cpp.o CMakeFiles/libgromacs.dir/utility/baseversion-gen.cpp.o CMakeFiles/libgromacs.dir/fileio/checkpoint.cpp.o CMakeFiles/libgromacs.dir/fileio/confio.cpp.o CMakeFiles/libgromacs.dir/fileio/enxio.cpp.o CMakeFiles/libgromacs.dir/fileio/espio.cpp.o CMakeFiles/libgromacs.dir/fileio/filetypes.cpp.o CMakeFiles/libgromacs.dir/fileio/g96io.cpp.o CMakeFiles/libgromacs.dir/fileio/gmx_internal_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio.cpp.o CMakeFiles/libgromacs.dir/fileio/gmxfio_xdr.cpp.o CMakeFiles/libgromacs.dir/fileio/groio.cpp.o CMakeFiles/libgromacs.dir/fileio/libxdrf.cpp.o CMakeFiles/libgromacs.dir/fileio/matio.cpp.o CMakeFiles/libgromacs.dir/fileio/md5.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymap.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcdensitymapheader.cpp.o CMakeFiles/libgromacs.dir/fileio/mrcserializer.cpp.o CMakeFiles/libgromacs.dir/fileio/mtxio.cpp.o CMakeFiles/libgromacs.dir/fileio/oenv.cpp.o CMakeFiles/libgromacs.dir/fileio/pdbio.cpp.o CMakeFiles/libgromacs.dir/fileio/readinp.cpp.o CMakeFiles/libgromacs.dir/fileio/timecontrol.cpp.o CMakeFiles/libgromacs.dir/fileio/tngio.cpp.o CMakeFiles/libgromacs.dir/fileio/tpxio.cpp.o CMakeFiles/libgromacs.dir/fileio/trrio.cpp.o CMakeFiles/libgromacs.dir/fileio/trxio.cpp.o CMakeFiles/libgromacs.dir/fileio/vmdio.cpp.o CMakeFiles/libgromacs.dir/fileio/warninp.cpp.o CMakeFiles/libgromacs.dir/fileio/writeps.cpp.o CMakeFiles/libgromacs.dir/fileio/xdrd.cpp.o CMakeFiles/libgromacs.dir/fileio/xtcio.cpp.o CMakeFiles/libgromacs.dir/fileio/xvgr.cpp.o CMakeFiles/libgromacs.dir/selection/centerofmass.cpp.o CMakeFiles/libgromacs.dir/selection/compiler.cpp.o CMakeFiles/libgromacs.dir/selection/evaluate.cpp.o CMakeFiles/libgromacs.dir/selection/indexutil.cpp.o CMakeFiles/libgromacs.dir/selection/mempool.cpp.o CMakeFiles/libgromacs.dir/selection/nbsearch.cpp.o CMakeFiles/libgromacs.dir/selection/params.cpp.o CMakeFiles/libgromacs.dir/selection/parsetree.cpp.o CMakeFiles/libgromacs.dir/selection/poscalc.cpp.o CMakeFiles/libgromacs.dir/selection/position.cpp.o CMakeFiles/libgromacs.dir/selection/scanner_internal.cpp.o CMakeFiles/libgromacs.dir/selection/selection.cpp.o CMakeFiles/libgromacs.dir/selection/selectioncollection.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoption.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionbehavior.cpp.o CMakeFiles/libgromacs.dir/selection/selectionoptionmanager.cpp.o CMakeFiles/libgromacs.dir/selection/selelem.cpp.o CMakeFiles/libgromacs.dir/selection/selhelp.cpp.o CMakeFiles/libgromacs.dir/selection/selmethod.cpp.o CMakeFiles/libgromacs.dir/selection/selvalue.cpp.o CMakeFiles/libgromacs.dir/selection/sm_compare.cpp.o CMakeFiles/libgromacs.dir/selection/sm_distance.cpp.o CMakeFiles/libgromacs.dir/selection/sm_insolidangle.cpp.o CMakeFiles/libgromacs.dir/selection/sm_keywords.cpp.o CMakeFiles/libgromacs.dir/selection/sm_merge.cpp.o CMakeFiles/libgromacs.dir/selection/sm_permute.cpp.o CMakeFiles/libgromacs.dir/selection/sm_position.cpp.o CMakeFiles/libgromacs.dir/selection/sm_same.cpp.o CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o CMakeFiles/libgromacs.dir/selection/symrec.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/eigensolver.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/matrix.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/nrjac.cpp.o linearalgebra/CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/constraintelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/domdechelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/energyelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/forceelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/propagator.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/signallers.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/topologyholder.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o modularsimulator/CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o selection/CMakeFiles/scanner.dir/parser.cpp.o selection/CMakeFiles/scanner.dir/scanner.cpp.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o
/usr/bin/ranlib ../../lib/libgromacs_mdrun_mpi.mpich.a
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[100%] Built target libgromacs
/usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich /<<PKGBUILDDIR>>/build/mpich/src/programs /<<PKGBUILDDIR>>/build/mpich/src/programs/CMakeFiles/mdrun.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -f src/programs/CMakeFiles/mdrun.dir/build.make src/programs/CMakeFiles/mdrun.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich'
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=0 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/mdrun.dir/mdrun_main.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun_main.cpp
cd /<<PKGBUILDDIR>>/build/mpich/src/programs && /usr/bin/cmake -E cmake_link_script CMakeFiles/mdrun.dir/link.txt --verbose=1
/usr/bin/mpicxx.mpich -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -Wl,-z,relro -Wl,-z,now CMakeFiles/mdrun.dir/mdrun_main.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -o ../../bin/mdrun_mpi.mpich ../../lib/libgromacs_mdrun_mpi.mpich.a /usr/lib/arm-linux-gnueabihf/libz.so /usr/lib/arm-linux-gnueabihf/libhwloc.so -lrt /usr/lib/arm-linux-gnueabihf/libfftw3f.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so /usr/lib/arm-linux-gnueabihf/libblas.so /usr/lib/arm-linux-gnueabihf/liblapack.so -lpthread -lm /usr/lib/gcc/arm-linux-gnueabihf/10/libgomp.so /usr/lib/arm-linux-gnueabihf/libpthread.so
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
[100%] Built target mdrun
make[2]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich/CMakeFiles 0
make[1]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich'
/usr/bin/make -j4 -C build/mpich-dp
make[1]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/cmake -S/<<PKGBUILDDIR>> -B/<<PKGBUILDDIR>>/build/mpich-dp --check-build-system CMakeFiles/Makefile.cmake 0
/usr/bin/cmake -E cmake_progress_start /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles /<<PKGBUILDDIR>>/build/mpich-dp//CMakeFiles/progress.marks
/usr/bin/make -f CMakeFiles/Makefile2 all
make[2]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/depend
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/depend
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/depend
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/thread_mpi.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/CMakeFiles/release-version-info.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/tng_io_obj.dir/DependInfo.cmake --color=
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection/CMakeFiles/scanner.dir/DependInfo.cmake --color=
Scanning dependencies of target release-version-info
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f CMakeFiles/release-version-info.dir/build.make CMakeFiles/release-version-info.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>> && /usr/bin/cmake -D PYTHON_EXECUTABLE=/usr/bin/python3 -D PROJECT_VERSION=2020.6-Raspbian-2020.6-2 -D PROJECT_SOURCE_DIR=/<<PKGBUILDDIR>> -D DIRECTORIES_TO_CHECKSUM=src:python_packaging -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo-partial.cmake.cmakein -D VERSION_OUT=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_STRING_OF_FORK=Raspbian-2020.6-2 -P /<<PKGBUILDDIR>>/cmake/gmxGenerateVersionInfoRelease.cmake
Scanning dependencies of target thread_mpi
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/thread_mpi.dir/build.make src/gromacs/CMakeFiles/thread_mpi.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/errhandler.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/errhandler.cpp
Scanning dependencies of target scanner
Scanning dependencies of target tng_io_obj
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/selection/CMakeFiles/scanner.dir/build.make src/gromacs/selection/CMakeFiles/scanner.dir/build
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/tng_io_obj.dir/build.make src/gromacs/CMakeFiles/tng_io_obj.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/parser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/parser.cpp
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwlzh.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwlzh.c
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 0%] Built target release-version-info
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/bwt.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/bwt.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/tmpi_malloc.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/tmpi_malloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/atomic.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/atomic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/lock.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/lock.cpp
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/lmfit_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target lmfit_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make src/gromacs/CMakeFiles/lmfit_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fPIC -std=c++14 -o CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o -c /<<PKGBUILDDIR>>/src/external/lmfit/lmmin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/pthreads.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/pthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/coder.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/coder.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/thread_mpi.dir/__/external/thread_mpi/src/system_error.cpp.o -c /<<PKGBUILDDIR>>/src/external/thread_mpi/src/system_error.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target thread_mpi
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/DependInfo.cmake --color=
Scanning dependencies of target linearalgebra
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build.make src/gromacs/linearalgebra/CMakeFiles/linearalgebra.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/eigensolver.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/eigensolver.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/dict.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/dict.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/fixpoint.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/fixpoint.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffman.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffman.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/gmx_arpack.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/gmx_arpack.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target lmfit_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/selection && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-unused -Wno-unused-parameter -Wno-missing-declarations -Wno-null-conversion -std=c++14 -o CMakeFiles/scanner.dir/scanner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/selection/scanner.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/huffmem.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/huffmem.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/lz77.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/lz77.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/merge_sort.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/merge_sort.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/mtf.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/mtf.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/rle.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/rle.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/tng_compress.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/tng_compress.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/vals16.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/vals16.c
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/DependInfo.cmake --color=
Scanning dependencies of target modularsimulator
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build.make src/gromacs/modularsimulator/CMakeFiles/modularsimulator.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/checkpointhelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp: In member function 'void gmx::CheckpointHelper::writeCheckpoint(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/checkpointhelper.cpp:129:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
129 | mdoutf_write_to_trajectory_files(fplog_, cr_, trajectoryElement_->outf_, MDOF_CPT,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
130 | globalNumAtoms_, step, time, localStateInstance_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
131 | state_global_, observablesHistory_, ArrayRef<RVec>());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/compositesimulatorelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/compositesimulatorelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/matrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/matrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/computeglobalselement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/computeglobalselement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/warnmalloc.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/warnmalloc.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/widemuldiv.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/widemuldiv.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc2.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc2.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/nrjac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/nrjac.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target scanner
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/compression/xtc3.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/compression/xtc3.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/linearalgebra && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -Wno-stringop-truncation -std=c++14 -o CMakeFiles/linearalgebra.dir/sparsematrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/linearalgebra/sparsematrix.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 1%] Built target linearalgebra
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/programs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/programs /<<PKGBUILDDIR>>/build/mpich-dp/src/programs/CMakeFiles/mdrun_objlib.dir/DependInfo.cmake --color=
Scanning dependencies of target mdrun_objlib
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/programs/CMakeFiles/mdrun_objlib.dir/build.make src/programs/CMakeFiles/mdrun_objlib.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/mdrun.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/mdrun.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/tng_io.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/tng_io.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/constraintelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/constraintelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicc.mpich -DGMX_DOUBLE=1 -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/external/tng_io/include -I/<<PKGBUILDDIR>>/build/mpich-dp/tng/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -o CMakeFiles/tng_io_obj.dir/__/external/tng_io/src/lib/md5.c.o -c /<<PKGBUILDDIR>>/src/external/tng_io/src/lib/md5.c
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/programs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -std=c++14 -o CMakeFiles/mdrun_objlib.dir/mdrun/nonbonded_bench.cpp.o -c /<<PKGBUILDDIR>>/src/programs/mdrun/nonbonded_bench.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/domdechelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/domdechelper.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/energyelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/forceelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 2%] Built target mdrun_objlib
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/freeenergyperturbationelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp: In member function 'void gmx::ForceElement::run(gmx::Step, gmx::Time, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/forceelement.cpp:159:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
159 | do_force(fplog_, cr_, ms, inputrec_, awh, enforcedRotation_, imdSession_, pull_work_, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
160 | nrnb_, wcycle_, localTopology_, box, x, hist, forces, force_vir, mdAtoms_->mdatoms(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
161 | energyElement_->enerdata(), fcd_, lambda, graph, fr_, runScheduleWork_, vsite_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
162 | energyElement_->muTot(), time, ed, static_cast<int>(flags), ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In static member function 'static _Res std::_Function_handler<_Res(_ArgTypes ...), _Functor>::_M_invoke(const std::_Any_data&, _ArgTypes&& ...) [with _Res = void; _Functor = gmx::FreeEnergyPerturbationElement::scheduleTask(gmx::Step, gmx::Time, const RegisterRunFunctionPtr&)::<lambda()>; _ArgTypes = {}]':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/modularsimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In constructor 'gmx::FreeEnergyPerturbationElement::FreeEnergyPerturbationElement(FILE*, const t_inputrec*, gmx::MDAtoms*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:68:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
68 | initialize_lambdas(fplog_, *inputrec_, true, ¤tFEPState_, lambda_, lambda0_.data());
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp: In member function 'void gmx::FreeEnergyPerturbationElement::updateLambdas(gmx::Step)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/freeenergyperturbationelement.cpp:86:27: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
86 | setCurrentLambdasLocal(step, inputrec_->fepvals, lambda0_.data(), lambda_, currentFEPState_);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/parrinellorahmanbarostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp: In member function 'void gmx::EnergyElement::doStep(gmx::Time, bool, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/energyelement.cpp:239:17: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
239 | sum_dhdl(enerd_, freeEnergyPerturbationElement_->constLambdaView(), *inputrec_->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/pmeloadbalancehelper.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp: In constructor 'gmx::ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int, int, real, gmx::Step, gmx::ArrayRef<double [3]>, gmx::PropagatorCallbackPtr, gmx::StatePropagatorData*, gmx::EnergyElement*, FILE*, const t_inputrec*, const gmx::MDAtoms*, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/parrinellorahmanbarostat.cpp:62:1: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
62 | ParrinelloRahmanBarostat::ParrinelloRahmanBarostat(int nstpcouple,
| ^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/propagator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/propagator.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp: In member function 'void gmx::PmeLoadBalanceHelper::run(gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/pmeloadbalancehelper.cpp:107:19: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
107 | pme_loadbal_do(pme_loadbal_, cr_, (isVerbose_ && MASTER(cr_)) ? stderr : nullptr, fplog_,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
108 | mdlog_, *inputrec_, fr_, statePropagatorData_->constBox(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
109 | statePropagatorData_->constPositionsView().paddedArrayRef(), wcycle_, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
110 | step - inputrec_->init_step, &bPMETunePrinting_, false);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/shellfcelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp: In member function 'void gmx::ShellFCElement::run(gmx::Step, gmx::Time, bool, unsigned int)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/shellfcelement.cpp:185:24: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
185 | relax_shell_flexcon(fplog_, cr_, ms, isVerbose_, enforcedRotation_, step, inputrec_, imdSession_,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
186 | pull_work_, isNSStep, static_cast<int>(flags), localTopology_, constr_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
187 | energyElement_->enerdata(), fcd_, statePropagatorData_->localNumAtoms(), x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
188 | v, box, lambda, hist, forces, force_vir, mdAtoms_->mdatoms(), nrnb_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
189 | wcycle_, graph, shellfc_, fr_, runScheduleWork_, time,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
190 | energyElement_->muTot(), vsite_, ddBalanceRegionHandler_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/signallers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/signallers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/statepropagatordata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/topologyholder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/topologyholder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/trajectoryelement.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/trajectoryelement.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::_ZN3gmx19StatePropagatorData24trajectoryWriterTeardownEP10gmx_mdoutf.part.0(gmx_mdoutf*)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:464:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
464 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:466:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
466 | dd_collect_vec(cr_->dd, localStateBackup_.get(), localStateBackup_->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 5%] Built target tng_io_obj
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/modularsimulator && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fopenmp -Wno-redundant-move -std=c++14 -o CMakeFiles/modularsimulator.dir/vrescalethermostat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp: In member function 'void gmx::StatePropagatorData::write(gmx_mdoutf_t, gmx::Step, gmx::Time)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:411:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
411 | mdoutf_write_to_trajectory_files(fplog_, cr_, outf, static_cast<int>(mdof_flags),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
412 | totalNumAtoms_, currentStep, currentTime,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
413 | localStateBackup_.get(), globalState_, observablesHistory, f_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/statepropagatordata.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/isimulator.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/modularsimulator/modularsimulator.cpp:44:
/usr/include/c++/10/bits/unique_ptr.h: In member function 'std::unique_ptr<gmx::ISimulatorElement> gmx::ModularSimulator::buildIntegrator(gmx::SignallerBuilder<gmx::NeighborSearchSignaller>*, gmx::SignallerBuilder<gmx::EnergySignaller>*, gmx::SignallerBuilder<gmx::LoggingSignaller>*, gmx::TrajectoryElementBuilder*, std::vector<gmx::ICheckpointHelperClient*>*, gmx::CheckBondedInteractionsCallbackPtr*, gmx::compat::not_null<gmx::StatePropagatorData*>, gmx::compat::not_null<gmx::EnergyElement*>, gmx::FreeEnergyPerturbationElement*, bool)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double [3]>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::StatePropagatorData::setLocalState(std::unique_ptr<t_state>)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp: In constructor 'gmx::VRescaleThermostat::VRescaleThermostat(int, int, bool, int64_t, int, double, const real*, const real*, const real*, gmx::EnergyElement*, gmx::ArrayRef<double>, gmx::PropagatorCallbackPtr, const t_state*, t_commrec*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/modularsimulator/vrescalethermostat.cpp:59:1: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
59 | VRescaleThermostat::VRescaleThermostat(int nstcouple,
| ^~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::StatePropagatorData::StatePropagatorData(int, FILE*, const t_commrec*, t_state*, int, int, int, int, bool, gmx::FreeEnergyPerturbationElement*, const gmx::TopologyHolder*, bool, bool, std::string, const t_inputrec*, const t_mdatoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
[ 8%] Built target modularsimulator
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/depend
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -D VERSION_VARIABLES=/<<PKGBUILDDIR>>/build/mpich-dp/VersionInfo.cmake -D VERSION_CMAKEIN=/<<PKGBUILDDIR>>/src/gromacs/utility/baseversion-gen.cpp.cmakein -D VERSION_OUT=utility/baseversion-gen.cpp -D GMX_SOURCE_DOI= -D GMX_RELEASE_HASH= -D GMX_SOURCE_HASH= -P /<<PKGBUILDDIR>>/cmake/gmxConfigureVersionInfo.cmake
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/cmake -E touch utility/baseversion-gen.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /<<PKGBUILDDIR>> /<<PKGBUILDDIR>>/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs/CMakeFiles/libgromacs.dir/DependInfo.cmake --color=
Scanning dependencies of target libgromacs
make[3]: Leaving directory '/<<PKGBUILDDIR>>/build/mpich-dp'
/usr/bin/make -f src/gromacs/CMakeFiles/libgromacs.dir/build.make src/gromacs/CMakeFiles/libgromacs.dir/build
make[3]: Entering directory '/<<PKGBUILDDIR>>/build/mpich-dp'
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/alignedallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/alignedallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/any.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/any.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/basenetwork.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/basenetwork.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/baseversion.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/baseversion.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/binaryinformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/binaryinformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/compare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/compare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/coolstuff.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/coolstuff.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/cstringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/cstringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/datafilefinder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/datafilefinder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/directoryenumerator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/directoryenumerator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorcodes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorcodes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/errorformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/errorformat.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/exceptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/exceptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fatalerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/fileredirector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/fileredirector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/filestream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/filestream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/futil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/futil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxassert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxassert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/gmxomp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/gmxomp.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/ikeyvaluetreeerror.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/ikeyvaluetreeerror.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/init.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/init.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/inmemoryserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/inmemoryserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/int64_to_int.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/int64_to_int.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetree.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetree.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreemdpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreemdpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreeserializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreeserializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/keyvaluetreetransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/keyvaluetreetransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/logger.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/logger.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/loggerbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/loggerbuilder.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/messagestringcollector.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/messagestringcollector.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/mpiinplacebuffers.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/mpiinplacebuffers.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/niceheader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/niceheader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/path.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/path.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/physicalnodecommunicator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/physicalnodecommunicator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/pleasecite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/pleasecite.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/programcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/programcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/smalloc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/smalloc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strconvert.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strconvert.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/strdb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/strdb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringstream.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringstream.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/stringutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/sysinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/sysinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textreader.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textreader.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/textwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/textwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/utility/txtdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/utility/txtdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/atomdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/benchmark/bench_system.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp: In function 'void Nbnxm::setupAndRunInstance(const gmx::BenchmarkSystem&, const Nbnxm::KernelBenchOptions&, bool)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:222:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
222 | nbnxn_put_on_grid(nbv.get(), system.box, 0, lowerCorner, upperCorner, nullptr,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
223 | { 0, int(system.coordinates.size()) }, atomDensity, atomInfo,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | system.coordinates, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp: In function 'void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/atomdata.cpp:1484:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1484 | void nbnxn_atomdata_add_nbat_fshift_to_fshift(const nbnxn_atomdata_t& nbat, gmx::ArrayRef<gmx::RVec> fshift)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const Nbnxm::KernelBenchOptions&}; _Tp = Nbnxm::KernelBenchOptions; _Alloc = std::allocator<Nbnxm::KernelBenchOptions>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<Nbnxm::KernelBenchOptions>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_setup.cpp:50:
/usr/include/c++/10/bits/stl_vector.h: In function 'void Nbnxm::bench(int, const Nbnxm::KernelBenchOptions&)':
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<Nbnxm::KernelBenchOptions*, std::vector<Nbnxm::KernelBenchOptions> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/gridset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernel_common.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernel_common.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In function '_ZN5Nbnxm7GridSet9putOnGridEPA3_KdiPS1_S4_PKN3gmx15UpdateGroupsCogENS5_5RangeIiEEdNS5_8ArrayRefIKiEENSB_IKNS5_11BasicVectorIdEEEEiPSC_P16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:216:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
216 | Grid::calcColumnIndices(grid.dimensions(), updateGroupsCog, atomRange, x, ddZone, move, thread,
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
217 | nthread, gridSetData_.cells, gridWork_[thread].numAtomsPerColumn);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp: In member function 'void Nbnxm::GridSet::putOnGrid(const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:136:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
136 | void GridSet::putOnGrid(const matrix box,
| ^~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/gridset.cpp:223:24: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
223 | grid.setCellIndices(ddZone, cellOffset, &gridSetData_, gridWork_, atomRange, atomInfo.data(), x,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
224 | numAtomsMoved, nbat);
| ~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::fillCell(Nbnxm::GridSetData*, nbnxn_atomdata_t*, int, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, Nbnxm::BoundingBox*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:859:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
859 | void Grid::fillCell(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsCpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:987:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
987 | void Grid::sortColumnsCpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::sortColumnsGpuGeometry(Nbnxm::GridSetData*, int, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, nbnxn_atomdata_t*, gmx::Range<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1050:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1050 | void Grid::sortColumnsGpuGeometry(GridSetData* gridSetData,
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In function '_ZN5Nbnxm4Grid14setCellIndicesEiiPNS_11GridSetDataEN3gmx8ArrayRefINS_8GridWorkEEENS3_5RangeIiEEPKiNS4_IKNS3_11BasicVectorIdEEEEiP16nbnxn_atomdata_t._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1409:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1409 | sortColumnsGpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1410 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1404:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1404 | sortColumnsCpuGeometry(gridSetData, ddZone, atinfo, x, nbat, columnRange,
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1405 | gridWork[thread].sortBuffer);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In static member function 'static void Nbnxm::Grid::calcColumnIndices(const Nbnxm::Grid::Dimensions&, const gmx::UpdateGroupsCog*, gmx::Range<int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*, int, int, gmx::ArrayRef<int>, gmx::ArrayRef<int>)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1172:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1172 | void Grid::calcColumnIndices(const Grid::Dimensions& gridDims,
| ^~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_gpu_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp: In member function 'void nonbonded_verlet_t::dispatchNonbondedKernel(gmx::InteractionLocality, const interaction_const_t&, const gmx::StepWorkload&, int, const t_forcerec&, gmx_enerdata_t*, t_nrnb*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kerneldispatch.cpp:442:33: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
442 | nbnxn_kernel_gpu_ref(
| ~~~~~~~~~~~~~~~~~~~~^
443 | pairlistSet.gpuList(), nbat.get(), &ic, fr.shift_vec, stepWork, clearF,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
444 | nbat->out[0].f, nbat->out[0].fshift.data(), enerd->grpp.ener[egCOULSR].data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
445 | fr.bBHAM ? enerd->grpp.ener[egBHAMSR].data() : enerd->grpp.ener[egLJSR].data());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp: In member function 'void Nbnxm::Grid::setCellIndices(int, int, Nbnxm::GridSetData*, gmx::ArrayRef<Nbnxm::GridWork>, gmx::Range<int>, const int*, gmx::ArrayRef<const gmx::BasicVector<double> >, int, nbnxn_atomdata_t*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/grid.cpp:1286:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1286 | void Grid::setCellIndices(int ddZone,
| ^~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp: In function 'void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu*, const nbnxn_atomdata_t*, const interaction_const_t*, real (*)[3], const gmx::StepWorkload&, int, gmx::ArrayRef<double>, real*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_gpu_ref.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
57 | void nbnxn_kernel_gpu_ref(const NbnxnPairlistGpu* nbl,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_reference/kernel_ref_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_reference/kernel_ref_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_2xmm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_2xmm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEwTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecEw_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTabTwinCut_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecQSTab_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJCombLB_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJEwCombGeom_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJFSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJPSw_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_F.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_ElecRF_VdwLJ_VgrpF.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/kernels_simd_4xm/kernel_prune.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/kernels_simd_4xm/kernel_prune.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_geometry.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_geometry.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/nbnxm_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm_setup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid(nonbonded_verlet_t*, const real (*)[3], int, const real*, const real*, const gmx::UpdateGroupsCog*, gmx::Range<int>, real, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >, int, const int*)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:57:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
57 | void nbnxn_put_on_grid(nonbonded_verlet_t* nb_verlet,
| ^~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In function 'void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t*, const gmx_domdec_zones_t*, gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:76:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
76 | void nbnxn_put_on_grid_nonlocal(nonbonded_verlet_t* nbv,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:53:
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.h:184:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
184 | gridSet_.putOnGrid(box, ddZone, lowerCorner, upperCorner, updateGroupsCog, atomRange,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
185 | atomDensity, atomInfo, x, numAtomsMoved, move, nbat);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::convertCoordinates(gmx::AtomLocality, bool, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
126 | void nonbonded_verlet_t::convertCoordinates(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:126:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp: In member function 'void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(gmx::AtomLocality, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/nbnxm/nbnxm.cpp:159:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
159 | void nonbonded_verlet_t::atomdata_add_nbat_f_to_f(const gmx::AtomLocality locality,
| ^~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlist_tuning.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist_tuning.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistparams.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairlistset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlistset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/pairsearch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairsearch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/nbnxm/prunekerneldispatch.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/nbnxm/prunekerneldispatch.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinehelpwriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinehelpwriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineinit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineinit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlinemodulemanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlinemodulemanager.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/pairlist.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::PinningPolicy}; _Tp = NbnxnPairlistGpu; _Alloc = std::allocator<NbnxnPairlistGpu>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<NbnxnPairlistGpu>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'PairlistSet::PairlistSet(gmx::InteractionLocality, const PairlistParams&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<NbnxnPairlistGpu*, std::vector<NbnxnPairlistGpu> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineoptionsmodule.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineoptionsmodule.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/cmdlineprogramcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/cmdlineprogramcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/filenm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/pargs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/pargs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/shellcompletions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/shellcompletions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/commandline/viewit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/commandline/viewit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/atomdistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/atomdistribution.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/box.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/cellsizes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/cellsizes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/collect.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void low_set_ddbox(int, int, const int (*)[3], const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const MPI_Comm*, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:232:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
232 | static void low_set_ddbox(int numPbcDimensions,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox(const gmx_domdec_t&, bool, const real (*)[3], bool, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:278:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
278 | void set_ddbox(const gmx_domdec_t& dd,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
291 | low_set_ddbox(dd.unitCellInfo.npbcdim, dd.unitCellInfo.numBoundedDimensions, &dd.nc, box,
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
292 | calculateUnboundedSize, xRef,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | needToReduceCoordinateData ? &dd.mpi_comm_all : nullptr, ddbox);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:291:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp: In function 'void set_ddbox_cr(const t_commrec&, const int (*)[3], const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:302:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
302 | void set_ddbox_cr(const t_commrec& cr,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/box.cpp:311:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
311 | low_set_ddbox(ePBC2npbcdim(ir.ePBC), inputrec2nboundeddim(&ir), dd_nc, box, true, x, nullptr, ddbox);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/distribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_vec(gmx_domdec_t*, const t_state*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
228 | void dd_collect_vec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:228:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp: In function 'void dd_collect_state(gmx_domdec_t*, const t_state*, t_state*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:291:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
291 | dd_collect_vec(dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:296:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
296 | dd_collect_vec(dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/collect.cpp:301:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
301 | dd_collect_vec(dd, state_local, state_local->cg_p, globalCgpRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dlbtiming.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dlbtiming.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeVec(gmx_domdec_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
143 | static void distributeVec(gmx_domdec_t* dd,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:143:13: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp: In function 'void distributeState(const gmx::MDLogger&, gmx_domdec_t*, const gmx_mtop_t&, t_state*, const gmx_ddbox_t&, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
259 | distributeVec(dd, DDMASTER(dd) ? state->x : gmx::ArrayRef<const gmx::RVec>(), state_local->x);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:259:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
263 | distributeVec(dd, DDMASTER(dd) ? state->v : gmx::ArrayRef<const gmx::RVec>(), state_local->v);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:263:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
267 | distributeVec(dd, DDMASTER(dd) ? state->cg_p : gmx::ArrayRef<const gmx::RVec>(), state_local->cg_p);
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/distribute.cpp:267:22: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_constraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_constraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = double]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
118 | void ddSendrecv(const gmx_domdec_t* dd,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp: In function 'void ddSendrecv(const gmx_domdec_t*, int, int, gmx::ArrayRef<T>, gmx::ArrayRef<T>) [with T = gmx::BasicVector<double>]':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_network.cpp:118:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_setup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool test_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3156:17: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3156 | static gmx_bool test_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3166:14: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3166 | set_ddbox(*dd, false, box, true, x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp: In function 'DDGridSetup getDDGridSetup(const gmx::MDLogger&, const t_commrec*, int, const gmx::DomdecOptions&, const DDSettings&, const DDSystemInfo&, real, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_ddbox_t*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:906:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
906 | DDGridSetup getDDGridSetup(const gmx::MDLogger& mdlog,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:934:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
934 | set_ddbox_cr(*cr, &numDomainsLegacyIvec, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_setup.cpp:938:21: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
938 | set_ddbox_cr(*cr, nullptr, ir, box, xGlobal, ddbox);
| ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'gmx_bool change_dd_cutoff(t_commrec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, real)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3228:10: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3228 | gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested)
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_specatomcomm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_specatomcomm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_topology.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::Impl::Impl(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3045:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3045 | DomainDecompositionBuilder::Impl::Impl(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:2967:82: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2967 | gridSetupCellsizeLimit, mtop, ir, box, xGlobal, &ddbox);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3091:92: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3091 | gridSetupCellsizeLimit, mtop_, ir_, box, xGlobal, &ddbox_);
| ^
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In constructor 'gmx::DomainDecompositionBuilder::DomainDecompositionBuilder(const gmx::MDLogger&, t_commrec*, const gmx::DomdecOptions&, const gmx::MdrunOptions&, bool, const gmx_mtop_t&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3134:1: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3134 | DomainDecompositionBuilder::DomainDecompositionBuilder(const MDLogger& mdlog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:3143:95: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3143 | impl_(new Impl(mdlog, cr, options, mdrunOptions, prefer1DAnd1Pulse, mtop, ir, box, xGlobal))
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/domdec_vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/domdec_vsite.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_spread_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
531 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:531:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_atom_sum_real(gmx_domdec_t*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
595 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:595:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_x(gmx_domdec_t*, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:272:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
272 | void dd_move_x(gmx_domdec_t* dd, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_wallcycle* wcycle)
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
349 | ddSendrecv(dd, d, dddirBackward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:349:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp: In function 'void dd_move_f(gmx_domdec_t*, gmx::ForceWithShiftForces*, gmx_wallcycle*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
424 | ddSendrecv(dd, d, dddirForward, sendBuffer, receiveBuffer);
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/domdec.cpp:424:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/dump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/dump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/ga2la.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/ga2la.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/gpuhaloexchange_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/gpuhaloexchange_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomset.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomset.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetdata.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetdata.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/localatomsetmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/localatomsetmanager.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/mdsetup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/mdsetup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/partition.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/redistribute.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/domdec/utility.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.h:45,
from /<<PKGBUILDDIR>>/src/gromacs/domdec/utility.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void dd_resize_state(t_state*, PaddedHostVector<gmx::BasicVector<double> >*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/3dtransforms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/3dtransforms.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_move_cellx(gmx_domdec_t*, const gmx_ddbox_t*, real*, real*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | ddSendrecv(dd, d, dddirBackward, gmx::arrayRefFromArray(&buf_s[0].min0, numReals),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
254 | gmx::arrayRefFromArray(&buf_r[0].min0, numReals));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/coordinatetransformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfit.cpp
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::scale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:65:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
65 | void ScaleCoordinates::Impl::scale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::Impl::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:75:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
75 | void ScaleCoordinates::Impl::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:97:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
97 | void ScaleCoordinates::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::ScaleCoordinates::inverseIgnoringZeroScale(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:102:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
102 | void ScaleCoordinates::inverseIgnoringZeroScale(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:104:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
104 | impl_->inverseIgnoringZeroScale(coordinates);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::Impl::transform(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:140:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
140 | void TranslateAndScale::Impl::transform(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp: In member function 'void gmx::TranslateAndScale::operator()(gmx::ArrayRef<gmx::BasicVector<double> >) const':
/<<PKGBUILDDIR>>/src/gromacs/math/coordinatetransformation.cpp:161:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
161 | void TranslateAndScale::operator()(ArrayRef<RVec> coordinates) const
| ^~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/densityfittingforce.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/densityfittingforce.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void setup_dd_communication(gmx_domdec_t*, real (*)[3], gmx_ddbox_t*, t_forcerec*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
2104 | ddSendrecv<gmx::RVec>(dd, dim_ind, dddirBackward, work.positionBuffer, rvecBufferRef);
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2104:34: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/do_fit.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/do_fit.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/exponentialmovingaverage.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/exponentialmovingaverage.cpp
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp: In function 'void dd_partition_system(FILE*, const gmx::MDLogger&, int64_t, const t_commrec*, gmx_bool, int, t_state*, const gmx_mtop_t&, const t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, PaddedHostVector<gmx::BasicVector<double> >*, gmx::MDAtoms*, gmx_localtop_t*, t_forcerec*, gmx_vsite_t*, gmx::Constraints*, t_nrnb*, gmx_wallcycle*, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2866:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2866 | set_ddbox(*dd, true, DDMASTER(dd) ? state_global->box : nullptr, true, xGlobal, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2907:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2907 | set_ddbox(*dd, bMasterState, state_local->box, true, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2928:18: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2928 | set_ddbox(*dd, bMasterState, state_local->box, bNStGlobalComm, state_local->x, &ddbox);
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2946 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2947 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home), state_local->x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2946:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
2970 | comm->updateGroupsCog->addCogs(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
2971 | gmx::arrayRefFromArray(dd->globalAtomGroupIndices.data(), dd->ncg_home),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2972 | state_local->x);
| ~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:2970:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/domdec/partition.cpp:3005:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
3005 | nbnxn_put_on_grid(fr->nbv.get(), state_local->box, 0, comm->zones.size[0].bb_x0,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3006 | comm->zones.size[0].bb_x1, comm->updateGroupsCog.get(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3007 | { 0, dd->ncg_home }, comm->zones.dens_zone0, fr->cginfo, state_local->x,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
3008 | ncg_moved, bRedist ? comm->movedBuffer.data() : nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/functions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/functions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/gausstransform.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/gausstransform.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/invertmatrix.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/invertmatrix.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/units.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/units.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/veccompare.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/veccompare.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/math/vecdump.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/math/vecdump.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/df_history.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/df_history.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/group.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/group.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/iforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/iforceprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -Wno-class-memaccess -o CMakeFiles/libgromacs.dir/mdtypes/inputrec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/inputrec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/md_enums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/md_enums.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/observableshistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/observableshistory.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdtypes/state.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpformat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpformat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'real (* makeRvecArray(gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::index))[3]':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:208:7: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
208 | rvec* makeRvecArray(gmx::ArrayRef<const gmx::RVec> v, gmx::index n)
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp: In function 'void initialize_lambdas(FILE*, const t_inputrec&, bool, int*, gmx::ArrayRef<double>, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:282:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
282 | void initialize_lambdas(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void init_gtc_state(t_state*, int, int, int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpmanager.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpmanager.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.h:59,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/state.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void state_change_natoms(t_state*, int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helptopic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helptopic.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/helpwritercontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/helpwritercontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/onlinehelp/rstparser.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/onlinehelp/rstparser.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/boxutilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/boxutilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/mshift.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/mshift.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbc_simd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc_simd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcenums.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcenums.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1394:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1394 | void put_atoms_in_box(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_box_omp(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >, int)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1454:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1454 | void put_atoms_in_box_omp(int ePBC, const matrix box, gmx::ArrayRef<gmx::RVec> x, gmx_unused int nth)
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_triclinic_unitcell(int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1470:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1470 | void put_atoms_in_triclinic_unitcell(int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp: In function 'void put_atoms_in_compact_unitcell(int, int, const real (*)[3], gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1527 | void put_atoms_in_compact_unitcell(int ePBC, int ecenter, const matrix box, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbc.cpp:1527:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/pbcmethods.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pbcutil/rmpbc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pbcutil/rmpbc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/seed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/seed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/random/tabulatednormaldistribution.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/random/tabulatednormaldistribution.cpp
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_molecule_com_in_box(int, int, t_block*, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
289 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:289:46: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp: In function 'void put_residue_com_in_box(int, int, int, t_atom*, int, real (*)[3], real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
341 | put_atoms_in_compact_unitcell(ePBC, ecenter, box, newComArrayRef);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pbcutil/pbcmethods.cpp:341:50: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/cubicsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/forcetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/forcetable.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/quadraticsplinetable.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp: In constructor 'gmx::CubicSplineTable::CubicSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
383 | CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/cubicsplinetable.cpp:383:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp: In constructor 'gmx::QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<gmx::NumericalSplineTableInput>, const std::pair<double, double>&, real)':
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:367:1: note: parameter passing for argument of type 'std::initializer_list<gmx::NumericalSplineTableInput>' changed in GCC 7.1
367 | QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/quadraticsplinetable.cpp:170:99: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
170 | std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/tables/splineutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/cyclecounter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/cyclecounter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/wallcycle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/wallcycle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/timing/walltime_accounting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/timing/walltime_accounting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomprop.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndSecondDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:211:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
211 | real findSmallestQuotientOfFunctionAndSecondDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'real gmx::internal::findSmallestQuotientOfFunctionAndThirdDerivative(gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:291:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
291 | real findSmallestQuotientOfFunctionAndThirdDerivative(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'void gmx::internal::throwUnlessDerivativeIsConsistentWithFunction(gmx::ArrayRef<const double>, gmx::ArrayRef<const double>, double, const std::pair<double, double>&)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
112 | void throwUnlessDerivativeIsConsistentWithFunction(ArrayRef<const double> function,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:112:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp: In function 'std::vector<double> gmx::internal::vectorSecondDerivative(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/tables/splineutil.cpp:310:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
310 | std::vector<double> vectorSecondDerivative(ArrayRef<const double> f, double spacing)
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atoms.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/utility/fatalerror.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/topology/atomprop.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {BaseEntry}; _Tp = BaseEntry; _Alloc = std::allocator<BaseEntry>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<BaseEntry>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/atomsbuilder.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/atomsbuilder.cpp
/usr/include/c++/10/bits/vector.tcc: In function 'void readProperty(AtomProperty*, ResidueType*, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<BaseEntry*, std::vector<BaseEntry> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/block.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/block.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/exclusionblocks.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/exclusionblocks.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/forcefieldparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/forcefieldparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/idef.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/idef.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/ifunc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/ifunc.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/index.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/index.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/invblock.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/invblock.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/mtop_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/mtop_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/residuetypes.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/residuetypes.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/symtab.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/symtab.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/topology/topsort.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/topology/topsort.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/swap/swapcoords.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/essentialdynamics/edsam.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/output.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/output.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/swap/swapcoords.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::LocalAtomSet}; _Tp = swap_group; _Alloc = std::allocator<swap_group>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<swap_group>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 't_swap* init_swapcoords(FILE*, const t_inputrec*, const char*, gmx_mtop_t*, const t_state*, ObservablesHistory*, t_commrec*, gmx::LocalAtomSetManager*, const gmx_output_env_t*, const gmx::MdrunOptions&, gmx::StartingBehavior)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<swap_group*, std::vector<swap_group> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pull_rotation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pull_rotation.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/essentialdynamics/edsam.cpp:48:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {edpar&}; _Tp = edpar; _Alloc = std::allocator<edpar>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<edpar>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::unique_ptr<gmx::EssentialDynamics> ed_open(int, ObservablesHistory*, const char*, const char*, gmx::StartingBehavior, const gmx_output_env_t*, const t_commrec*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<edpar*, std::vector<edpar> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/pulling/pullutil.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_group&, gmx::LocalAtomSet, const bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {t_pull_coord&}; _Tp = pull_coord_work_t; _Alloc = std::allocator<pull_coord_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_coord_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const t_pull_group&, const gmx::LocalAtomSet&, bool&}; _Tp = pull_group_work_t; _Alloc = std::allocator<pull_group_work_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In function 'pull_t* init_pull(FILE*, const pull_params_t*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, gmx::LocalAtomSetManager*, real)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_coord_work_t*, std::vector<pull_coord_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.h:57,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:40:
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pull_group_work_t*, std::vector<pull_group_work_t> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
2293 | }
| ^
/<<PKGBUILDDIR>>/src/gromacs/pulling/pull.cpp:2293:1: note: parameter passing for argument of type 'std::vector<pull_group_work_t>::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/awh.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp: In function 'bool pullCheckPbcWithinGroup(const pull_t&, gmx::ArrayRef<const gmx::BasicVector<double> >, const t_pbc&, int, real)':
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
949 | bool pullCheckPbcWithinGroup(const pull_t& pull,
| ^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:949:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/stringutil.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/pulling/pullutil.cpp:45:
/usr/include/c++/10/bits/stl_vector.h: In function 'void allocStatePrevStepPullCom(t_state*, const pull_t*)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/bias.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasparams.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, const double&, const double&}; _Tp = gmx::DimParams; _Alloc = std::allocator<gmx::DimParams>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::DimParams>::iterator' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.h:53,
from /<<PKGBUILDDIR>>/src/gromacs/awh/biasparams.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double}; _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'void gmx::Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:386:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
386 | void Bias::updateForceCorrelationGrid(gmx::ArrayRef<const double> probWeightNeighbor, double t)
| ^~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:406:45: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
406 | state_.calcUmbrellaForceAndPotential(dimParams_, grid_, indexNeighbor, forceFromNeighbor);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:70:
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.h:104:37: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
104 | tensors_[pointIndex].addData(weight, data, blockLengthMeasure == BlockLengthMeasure::Weight, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::BiasParams::BiasParams(const gmx::AwhParams&, const gmx::AwhBiasParams&, const std::vector<gmx::DimParams>&, double, double, gmx::BiasParams::DisableUpdateSkips, int, const std::vector<gmx::GridAxis>&, int)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biassharing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biassharing.cpp
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {gmx::Bias, std::vector<int, std::allocator<int> >&}; _Tp = gmx::BiasCoupledToSystem; _Alloc = std::allocator<gmx::BiasCoupledToSystem>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BiasCoupledToSystem>::iterator' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp: In member function 'gmx::ArrayRef<const double> gmx::Bias::calcForceAndUpdateBias(const double*, double*, double*, const t_commrec*, const gmx_multisim_t*, double, int64_t, int64_t, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:144:39: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
144 | updateForceCorrelationGrid(probWeightNeighbor, t);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
162 | state_.calcConvolvedForce(dimParams_, grid_, probWeightNeighbor, tempForce_, biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:162:34: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:172:57: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
172 | potential = state_.calcUmbrellaForceAndPotential(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | dimParams_, grid_, coordState.umbrellaGridpoint(), biasForce_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
182 | double newPotential = state_.moveUmbrella(dimParams_, grid_, probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
183 | biasForce_, step, seed, params_.biasIndex);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/bias.cpp:182:54: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Awh::Awh(FILE*, const t_inputrec&, const t_commrec*, const gmx_multisim_t*, const gmx::AwhParams&, const string&, pull_t*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::DimParams*, std::vector<gmx::DimParams> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BiasCoupledToSystem*, std::vector<gmx::BiasCoupledToSystem> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biasstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/biaswriter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/biaswriter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/coordstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In function 'void gmx::{anonymous}::updateTargetDistribution(gmx::ArrayRef<gmx::PointState>, const gmx::BiasParams&)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:292:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::PointState>' changed in GCC 7.1
292 | void updateTargetDistribution(gmx::ArrayRef<PointState> pointState, const BiasParams& params)
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp: In member function 'void gmx::CoordState::sampleUmbrellaGridpoint(const gmx::Grid&, int, gmx::ArrayRef<const double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/coordstate.cpp:129:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
129 | void CoordState::sampleUmbrellaGridpoint(const Grid& grid,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::calcUmbrellaForceAndPotential(const std::vector<gmx::DimParams>&, const gmx::Grid&, int, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:416:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
416 | double BiasState::calcUmbrellaForceAndPotential(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::calcConvolvedForce(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, gmx::ArrayRef<double>) const':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
437 | void BiasState::calcConvolvedForce(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:437:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'double gmx::BiasState::moveUmbrella(const std::vector<gmx::DimParams>&, const gmx::Grid&, gmx::ArrayRef<const double>, gmx::ArrayRef<double>, int64_t, int64_t, int)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
467 | double BiasState::moveUmbrella(const std::vector<DimParams>& dimParams,
| ^~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:467:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
476 | coordState_.sampleUmbrellaGridpoint(grid, coordState_.gridpointIndex(), probWeightNeighbor,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
477 | step, seed, indexSeed);
| ~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:476:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleProbabilityWeights(const gmx::Grid&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1233:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1233 | void BiasState::sampleProbabilityWeights(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor)
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::sampleCoordAndPmf(const gmx::Grid&, gmx::ArrayRef<const double>, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1287:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1287 | void BiasState::sampleCoordAndPmf(const Grid& grid, gmx::ArrayRef<const double> probWeightNeighbor, double convolvedBias)
| ^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationhistory.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationhistory.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp: In member function 'void gmx::BiasState::updateFreeEnergyAndAddSamplesToHistogram(const std::vector<gmx::DimParams>&, const gmx::Grid&, const gmx::BiasParams&, const t_commrec*, const gmx_multisim_t*, double, int64_t, FILE*, std::vector<int>*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1072 | double newHistogramSize = histogramSize_.newHistogramSize(params, t, detectedCovering, points_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1073 | weightSumCovering_, fplog);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/awh/biasstate.cpp:1072:62: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/correlationtensor.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/histogramsize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp: In member function 'void gmx::CorrelationTensor::addData(double, gmx::ArrayRef<const double>, bool, double)':
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
229 | void CorrelationTensor::addData(double weight, gmx::ArrayRef<const double> data, bool blockLengthInWeight, double t)
| ^~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:229:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.h:51,
from /<<PKGBUILDDIR>>/src/gromacs/awh/correlationtensor.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {int&, double}; _Tp = gmx::CorrelationBlockData; _Alloc = std::allocator<gmx::CorrelationBlockData>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::CorrelationBlockData>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::CorrelationTensor::CorrelationTensor(int, int, double)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::CorrelationBlockData*, std::vector<gmx::CorrelationBlockData> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSizeInitialStage(const gmx::BiasParams&, double, bool, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:77:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
77 | double HistogramSize::newHistogramSizeInitialStage(const BiasParams& params,
| ^~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp: In member function 'double gmx::HistogramSize::newHistogramSize(const gmx::BiasParams&, double, bool, const std::vector<gmx::PointState>&, gmx::ArrayRef<double>, FILE*)':
/<<PKGBUILDDIR>>/src/gromacs/awh/histogramsize.cpp:209:8: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
209 | double HistogramSize::newHistogramSize(const BiasParams& params,
| ^~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/pointstate.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/pointstate.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/awh/read_params.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/awh/read_params.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/dimparams.h:52,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.h:60,
from /<<PKGBUILDDIR>>/src/gromacs/awh/grid.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {double&, double&, double&, double&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/simd/support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/simd/support.cpp
/usr/include/c++/10/bits/vector.tcc: In constructor 'gmx::Grid::Grid(const std::vector<gmx::DimParams>&, const gmx::AwhDimParams*)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const double&, const double&, double, int&}; _Tp = gmx::GridAxis; _Alloc = std::allocator<gmx::GridAxis>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::GridAxis>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'void gmx::mapGridToDataGrid(std::vector<int>*, const double* const*, int, const string&, const gmx::Grid&, const string&)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::GridAxis*, std::vector<gmx::GridAxis> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imd.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imd.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/imd/imdsocket.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/imd/imdsocket.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/conformation_utilities.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/conformation_utilities.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/network.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/network.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nrnb.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nrnb.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gmxlib/nonbonded/nb_free_energy.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gmxlib/nonbonded/nb_free_energy.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/boxdeformation.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/broadcaststructs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp: In member function 'void gmx::BoxDeformation::apply(gmx::ArrayRef<gmx::BasicVector<double> >, real (*)[3], int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/boxdeformation.cpp:106:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
106 | void BoxDeformation::apply(ArrayRef<RVec> x, matrix box, int64_t step)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calc_verletbuf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/broadcaststructs.cpp:40:
/usr/include/c++/10/bits/stl_vector.h: In function 'void broadcastStateWithoutDynamics(const t_commrec*, t_state*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcmu.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.h:39,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/calc_verletbuf.cpp:38:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {VerletbufAtomtype}; _Tp = VerletbufAtomtype; _Alloc = std::allocator<VerletbufAtomtype>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<VerletbufAtomtype>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc: In function 'std::vector<VerletbufAtomtype> getVerletBufferAtomtypes(const gmx_mtop_t&, bool)':
/usr/include/c++/10/bits/vector.tcc:121:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<VerletbufAtomtype*, std::vector<VerletbufAtomtype> >' changed in GCC 7.1
121 | _M_realloc_insert(end(), std::forward<_Args>(__args)...);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp: In function 'void calc_mu(int, int, gmx::ArrayRef<gmx::BasicVector<double> >, const real*, const real*, int, double*, double*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/calcmu.cpp:50:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
50 | void calc_mu(int start,
| ^~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/calcvir.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/calcvir.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/checkpointhandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/checkpointhandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/compute_io.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/compute_io.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constr.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/constraintrange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
60 | static void constr_recur(const t_blocka* at2con,
| ^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp: In function 't_blocka gmx::make_at2con(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>, gmx::FlexibleConstraintTreatment)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constr.cpp:826:10: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
826 | t_blocka make_at2con(const gmx_moltype_t& moltype,
| ^~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp: In function 'void gmx::constr_recur(const t_blocka*, const InteractionLists&, gmx::ArrayRef<const t_iparams>, gmx_bool, int, int, int, int*, real, real, real*, int*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/constraintrange.cpp:60:13: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/coupling.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/dispersioncorrection.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:107:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
107 | DispersionCorrection::TopologyParams::TopologyParams(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp: In constructor 'DispersionCorrection::DispersionCorrection(const gmx_mtop_t&, const t_inputrec&, bool, int, gmx::ArrayRef<const double>, const interaction_const_t&, const char*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:520:1: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
520 | DispersionCorrection::DispersionCorrection(const gmx_mtop_t& mtop,
| ^~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/dispersioncorrection.cpp:530:85: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
530 | topParams_(mtop, inputrec, useBuckingham, numAtomTypes, nonbondedForceParameters)
| ^
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/ebin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp: In function 'void andersen_tcoupl(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, real, const std::vector<bool>&, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | void andersen_tcoupl(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/coupling.cpp:810:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp: In function 'void add_ebin_indexed(t_ebin*, int, gmx::ArrayRef<bool>, gmx::ArrayRef<const double>, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/ebin.cpp:197:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
197 | void add_ebin_indexed(t_ebin* eb,
| ^~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/enerdata_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/energyoutput.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp: In function 'void sum_dhdl(gmx_enerdata_t*, gmx::ArrayRef<const double>, const t_lambda&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/enerdata_utils.cpp:92:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
92 | void sum_dhdl(gmx_enerdata_t* enerd, gmx::ArrayRef<const real> lambda, const t_lambda& fepvals)
| ^~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/expanded_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/expanded_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/force.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp: In member function 'void gmx::EnergyOutput::addDataAtEnergyStep(bool, bool, double, real, const gmx_enerdata_t*, const t_state*, const t_lambda*, const t_expanded*, const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const real (*)[3], const gmx_ekindata_t*, const real*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/energyoutput.cpp:881:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
881 | add_ebin_indexed(ebin_, ie_, gmx::ArrayRef<bool>(bEner_), enerd->term, bSum);
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp: In function 'void do_force_lowlevel(t_forcerec*, const t_inputrec*, const t_idef*, const t_commrec*, const gmx_multisim_t*, t_nrnb*, gmx_wallcycle_t, const t_mdatoms*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ForceOutputs*, gmx_enerdata_t*, t_fcdata*, const real (*)[3], const real*, const t_graph*, const real (*)[3], const gmx::StepWorkload&, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
290 | status = gmx_pme_do(
| ~~~~~~~~~~^
291 | fr->pmedata,
| ~~~~~~~~~~~~
292 | gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
293 | md->homenr - fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~
294 | forceWithVirial.force_, md->chargeA, md->chargeB, md->sqrt_c6A,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
295 | md->sqrt_c6B, md->sigmaA, md->sigmaB, box, cr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
296 | DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
297 | DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0, nrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
298 | ewaldOutput.vir_q, ewaldOutput.vir_lj, &Vlr_q, &Vlr_lj,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
299 | lambda[efptCOUL], lambda[efptVDW], &ewaldOutput.dvdl[efptCOUL],
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
300 | &ewaldOutput.dvdl[efptVDW], pme_flags);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:290:40: note: parameter passing for argument of type 'const gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
325 | gmx_pme_calc_energy(
| ~~~~~~~~~~~~~~~~~~~^
326 | fr->pmedata,
| ~~~~~~~~~~~~
327 | coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
328 | gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
329 | &Vlr_q);
| ~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/force.cpp:325:40: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/forcerec.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/gmx_omp_nthreads.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/gmx_omp_nthreads.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/groupcoord.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/groupcoord.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/lincs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:103:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
103 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/md_support.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp
In file included from /usr/include/c++/10/memory:83,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/forcerec.cpp:39:
/usr/include/c++/10/bits/unique_ptr.h: In function 'void init_forcerec(FILE*, const gmx::MDLogger&, t_forcerec*, t_fcdata*, const t_inputrec*, const gmx_mtop_t*, const t_commrec*, real (*)[3], const char*, const char*, gmx::ArrayRef<const std::__cxx11::basic_string<char> >, const gmx_hw_info_t&, const gmx_device_info_t*, bool, bool, real, gmx_wallcycle*)':
/usr/include/c++/10/bits/unique_ptr.h:962:30: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
962 | { return unique_ptr<_Tp>(new _Tp(std::forward<_Args>(__args)...)); }
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function 'void gmx::lincs_update_atoms(gmx::Lincs*, int, real, gmx::ArrayRef<const double>, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*, real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
445 | static void lincs_update_atoms(Lincs* li,
| ^~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:445:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.1':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
708 | lincs_update_atoms(lincsd, th, 1.0, sol, r,
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
709 | (econq != ConstraintVariable::Force) ? invmass : nullptr, fp);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:708:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp: In function '_ZN3gmx15constrain_lincsEbRK10t_inputrecxPNS_5LincsERK9t_mdatomsPK9t_commrecPK14gmx_multisim_tPA3_KdPA3_dSI_SG_P5t_pbcdPddSI_bSI_NS_18ConstraintVariableEP6t_nrnbiPi._omp_fn.0':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1079:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1079 | lincs_update_atoms(lincsd, th, 1.0, mlambda, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1141:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1141 | lincs_update_atoms(lincsd, th, 1.0, blc_sol, r, invmass, xp);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:1148:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1148 | lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdatoms.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp: In function 'void setCurrentLambdasLocal(int64_t, const t_lambda*, const double*, gmx::ArrayRef<double>, int)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/md_support.cpp:400:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
400 | void setCurrentLambdasLocal(const int64_t step,
| ^~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdebin_bar.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdebin_bar.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdatoms.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function 'void atoms2md(const gmx_mtop_t*, const t_inputrec*, int, const int*, int, gmx::MDAtoms*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::MDAtoms::resize(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/lincs.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::set_lincs(const t_idef&, const t_mdatoms&, bool, const t_commrec*, gmx::Lincs*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/mdoutf.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/membed.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/membed.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/nsgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/nsgrid.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp: In function 'void mdoutf_write_to_trajectory_files(FILE*, const t_commrec*, gmx_mdoutf_t, int, int, int64_t, double, t_state*, t_state*, ObservablesHistory*, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:257:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
257 | void mdoutf_write_to_trajectory_files(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:282:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
282 | dd_collect_vec(cr->dd, state_local, state_local->x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:287:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
287 | dd_collect_vec(cr->dd, state_local, state_local->v, globalVRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/mdoutf.cpp:293:27: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
293 | dd_collect_vec(cr->dd, state_local, f_local,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
294 | gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/perf_est.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/perf_est.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gamess.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gamess.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_gaussian.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_gaussian.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_mopac.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_mopac.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qm_orca.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qm_orca.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/qmmm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/qmmm.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rbin.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/resethandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/resethandler.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'int add_binr(t_bin*, gmx::ArrayRef<const double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
103 | int add_binr(t_bin* b, gmx::ArrayRef<const real> r)
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:103:5: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp: In function 'void extract_binr(t_bin*, int, gmx::ArrayRef<double>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/rbin.cpp:160:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
160 | void extract_binr(t_bin* b, int index, gmx::ArrayRef<real> r)
| ^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/rf_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/rf_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/settle.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/settle.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/shake.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/shake.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sighandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sighandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/sim_util.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/simulationsignal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/simulationsignal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/splitter.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/splitter.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stat.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stat.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp: In function 'void do_force(FILE*, const t_commrec*, const gmx_multisim_t*, const t_inputrec*, gmx::Awh*, gmx_enfrot*, gmx::ImdSession*, pull_t*, int64_t, t_nrnb*, gmx_wallcycle_t, const gmx_localtop_t*, const real (*)[3], gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, gmx_enerdata_t*, t_fcdata*, gmx::ArrayRef<double>, t_graph*, t_forcerec*, gmx::MdrunScheduleWorkload*, const gmx_vsite_t*, real*, double, gmx_edsam*, int, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:895:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
895 | void do_force(FILE* fplog,
| ^~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1070:43: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1070 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1103:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1103 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1154:30: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | nbnxn_put_on_grid(nbv, box, 0, vzero, box_diag, nullptr, { 0, mdatoms->homenr }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1155 | fr->cginfo, x.unpaddedArrayRef(), 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1161:39: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1161 | nbnxn_put_on_grid_nonlocal(nbv, domdec_zones(cr->dd), fr->cginfo, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1243 | nbv->convertCoordinates(AtomLocality::Local, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1243:36: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1320:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1320 | stateGpu->copyCoordinatesFromGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1337:51: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1337 | stateGpu->copyCoordinatesToGpu(x.unpaddedArrayRef(), AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1345 | nbv->convertCoordinates(AtomLocality::NonLocal, false, x.unpaddedArrayRef());
| ~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1345:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1525:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1525 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
1526 | forceOut.forceWithShiftForces().shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1589:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1589 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1590 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1601:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1601 | stateGpu->copyForcesFromGpu(forceOut.forceWithShiftForces().force(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1602 | AtomLocality::NonLocal);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1613:57: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1613 | nbnxn_atomdata_add_nbat_fshift_to_fshift(*nbv->nbat, forceWithShiftForces.shiftForces());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1634:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1634 | stateGpu->copyForcesToGpu(forceOut.forceWithShiftForces().force(), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1771:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1771 | stateGpu->copyForcesToGpu(forceWithShift, locality);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/sim_util.cpp:1790:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1790 | stateGpu->copyForcesFromGpu(forceWithShift, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/stophandler.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/stophandler.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/tgroup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/tgroup.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/trajectory_writing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/update_constrain_cuda_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp: In function 'void do_md_trajectory_writing(FILE*, t_commrec*, int, const t_filenm*, int64_t, int64_t, double, t_inputrec*, t_state*, t_state*, ObservablesHistory*, const gmx_mtop_t*, t_forcerec*, gmx_mdoutf_t, const gmx::EnergyOutput&, gmx_ekindata_t*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool, gmx_bool, gmx_bool, gmx_bool, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:56:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
56 | void do_md_trajectory_writing(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/trajectory_writing.cpp:143:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
143 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
144 | state, state_global, observablesHistory, f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroups.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp: In member function 'void gmx::UpdateConstrainCuda::integrate(GpuEventSynchronizer*, real, bool, bool, real (*)[3], bool, gmx::ArrayRef<const t_grp_tcstat>, bool, float, const real (*)[3])':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update_constrain_cuda_impl.cpp:70:6: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
70 | void UpdateConstrainCuda::integrate(GpuEventSynchronizer* /* fReadyOnDevice */,
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/updategroupscog.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'void update_pcouple_after_coordinates(FILE*, int64_t, const t_inputrec*, const t_mdatoms*, const real (*)[3], const real (*)[3], const real (*)[3], real (*)[3], t_state*, t_nrnb*, gmx::Update*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1752:29: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1752 | upd->deform()->apply(localX, state->box, step);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp: In function 'gmx_bool update_randomize_velocities(const t_inputrec*, int64_t, const t_commrec*, const t_mdatoms*, gmx::ArrayRef<gmx::BasicVector<double> >, const gmx::Update*, const gmx::Constraints*)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1868:17: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1868 | extern gmx_bool update_randomize_velocities(const t_inputrec* ir,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1896 | andersen_tcoupl(ir, step, cr, md, v, rate, upd->sd()->randomize_group, upd->sd()->boltzfac);
| ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:1896:24: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const gmx::BasicVector<double>&}; _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp: In function 'gmx::RangePartitioning gmx::makeUpdateGroups(const gmx_moltype_t&, gmx::ArrayRef<const t_iparams>)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroups.cpp:338:26: note: parameter passing for argument of type 'gmx::ArrayRef<const t_iparams>' changed in GCC 7.1
338 | static RangePartitioning makeUpdateGroups(const gmx_moltype_t& moltype, gmx::ArrayRef<const t_iparams> iparams)
| ^~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp: In member function 'void gmx::UpdateGroupsCog::addCogs(gmx::ArrayRef<const int>, gmx::ArrayRef<const gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:80:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
80 | void UpdateGroupsCog::addCogs(gmx::ArrayRef<const int> globalAtomIndices,
| ^~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.h:46,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/updategroupscog.cpp:45:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vcm.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vcm.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> >::iterator' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/vsite.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/math/paddedvector.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.h:40,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/update.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::Update::Impl::Impl(const t_inputrec*, gmx::BoxDeformation*)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::Update::setNumAtoms(int)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::AlignedAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdlib/wall.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdlib/wall.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfitting.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfitting.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingamplitudelookup.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp: In function 'void constructVsitesGlobal(const gmx_mtop_t&, gmx::ArrayRef<gmx::BasicVector<double> >)':
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
741 | void constructVsitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
| ^~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:741:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingamplitudelookup.cpp:44:
/usr/include/c++/10/bits/stl_vector.h: In member function 'virtual const std::vector<double>& gmx::{anonymous}::UnitAmplitudes::operator()(const t_mdatoms&, gmx::ArrayRef<const int>)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingforceprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = std::allocator<gmx::BasicVector<double> >]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/topology/idef.h:43,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.h:44,
from /<<PKGBUILDDIR>>/src/gromacs/mdlib/vsite.cpp:39:
/usr/include/c++/10/bits/stl_vector.h: In function '_Z25split_vsites_over_threadsPK7t_ilistPK9t_iparamsPK9t_mdatomsP11gmx_vsite_t._omp_fn.0':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double> > >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In constructor 'gmx::DensityFittingForceProvider::Impl::Impl(const gmx::DensityFittingParameters&, gmx::basic_mdspan<const float, gmx::extents<-1, -1, -1> >, const gmx::TranslateAndScale&, const gmx::LocalAtomSet&, int, double, const gmx::DensityFittingForceProviderState&)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:79:19: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
79 | scaleToLattice({ &sigmaInLatticeCoordinates, &sigmaInLatticeCoordinates + 1 });
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:166:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
166 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
167 | { &referenceDensityCenter_, &referenceDensityCenter_ + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:171:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
171 | transformationToDensityLattice_({ &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:172:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
172 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^
173 | { &referenceDensityOriginShift, &referenceDensityOriginShift + 1 });
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp: In member function 'void gmx::DensityFittingForceProvider::Impl::calculateForces(const gmx::ForceProviderInput&, gmx::ForceProviderOutput*)':
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:210:36: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
210 | transformationToDensityLattice_(transformedCoordinates_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingforceprovider.cpp:258:82: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
258 | transformationToDensityLattice_.scaleOperationOnly().inverseIgnoringZeroScale(forces_);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingoutputprovider.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingoutputprovider.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/densityfittingparameters.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/densityfittingparameters.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/applied_forces/electricfield.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/applied_forces/electricfield.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/bonded.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/bonded.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/disre.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/disre.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/gpubonded_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/gpubonded_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_forces.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_forces.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/listed_internal.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/listed_internal.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/manage_threading.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/manage_threading.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/orires.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/orires.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/pairs.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/pairs.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/position_restraints.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/position_restraints.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/listed_forces/restcbt.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/listed_forces/restcbt.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/calculate_spline_moduli.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/calculate_spline_moduli.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/ewald_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/ewald_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/long_range_correction.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/long_range_correction.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gather.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gather.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_grid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_grid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_load_balancing.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_only.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_realloc_insert(std::vector<_Tp, _Alloc>::iterator, _Args&& ...) [with _Args = {const pme_setup_t&}; _Tp = pme_setup_t; _Alloc = std::allocator<pme_setup_t>]':
/usr/include/c++/10/bits/vector.tcc:426:7: note: parameter passing for argument of type 'std::vector<pme_setup_t>::iterator' changed in GCC 7.1
426 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_load_balance(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, double, interaction_const_t*, nonbonded_verlet_t*, gmx_pme_t**, int64_t)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:551:13: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
551 | static void pme_load_balance(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdtypes/forcerec.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:47:
/usr/include/c++/10/bits/stl_vector.h:1198:21: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<pme_setup_t*, std::vector<pme_setup_t> >' changed in GCC 7.1
1198 | _M_realloc_insert(end(), __x);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp: In function 'void pme_loadbal_do(pme_load_balancing_t*, t_commrec*, FILE*, FILE*, const gmx::MDLogger&, const t_inputrec&, t_forcerec*, const real (*)[3], gmx::ArrayRef<const gmx::BasicVector<double> >, gmx_wallcycle_t, int64_t, int64_t, gmx_bool*, bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:896:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
896 | void pme_loadbal_do(pme_load_balancing_t* pme_lb,
| ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_load_balancing.cpp:1035:25: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1035 | pme_load_balance(pme_lb, cr, fp_err, fp_log, mdlog, ir, box, x,
| ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1036 | pme_lb->cycles_c - cycles_prev, fr->ic, fr->nbv.get(), &fr->pmedata, step);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'void gmx_pme_calc_energy(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<const double>, real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
952 | void gmx_pme_calc_energy(gmx_pme_t* pme, gmx::ArrayRef<const gmx::RVec> x, gmx::ArrayRef<const real> q, real* V)
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:952:6: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp: In function 'void __static_initialization_and_destruction_0(int, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:104:16: warning: ignoring return value of 'char* getenv(const char*)' declared with attribute 'warn_unused_result' [-Wunused-result]
104 | (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp: In function 'int gmx_pme_do(gmx_pme_t*, gmx::ArrayRef<const gmx::BasicVector<double> >, gmx::ArrayRef<gmx::BasicVector<double> >, real*, real*, real*, real*, real*, real*, const real (*)[3], const t_commrec*, int, int, t_nrnb*, gmx_wallcycle*, real (*)[3], real (*)[3], real*, real*, real, real, real*, real*, int)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1004 | int gmx_pme_do(struct gmx_pme_t* pme,
| ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1004:5: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1154 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, coefficient);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1154:33: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1384 | do_redist_pos_coeffs(pme, cr, bFirst, coordinates, RedistC6);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1384:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1393 | do_redist_pos_coeffs(pme, cr, FALSE, coordinates, RedistSigma);
| ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme.cpp:1393:37: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_redistribute.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = gmx::Allocator<double, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:72:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h: In function 'int gmx_pmeonly(gmx_pme_t*, const t_commrec*, t_nrnb*, gmx_wallcycle*, gmx_walltime_accounting_t, t_inputrec*, PmeRunMode)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double, gmx::Allocator<double, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:711:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
711 | stateGpu->copyCoordinatesToGpu(gmx::ArrayRef<gmx::RVec>(pme_pp->x), gmx::AtomLocality::All);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
728 | gmx_pme_do(pme, pme_pp->x, pme_pp->f, pme_pp->chargeA.data(), pme_pp->chargeB.data(),
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
729 | pme_pp->sqrt_c6A.data(), pme_pp->sqrt_c6B.data(), pme_pp->sigmaA.data(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
730 | pme_pp->sigmaB.data(), box, cr, maxshift_x, maxshift_y, mynrnb, wcycle,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
731 | output.coulombVirial_, output.lennardJonesVirial_, &output.coulombEnergy_,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
732 | &output.lennardJonesEnergy_, lambda_q, lambda_lj, &dvdlambda_q,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
733 | &dvdlambda_lj, pmeFlags);
| ~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_only.cpp:728:23: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_solve.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_solve.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void dd_pmeredist_f(gmx_pme_t*, PmeAtomComm*, gmx::ArrayRef<gmx::BasicVector<double> >, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:388:6: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
388 | void dd_pmeredist_f(struct gmx_pme_t* pme, PmeAtomComm* atc, gmx::ArrayRef<gmx::RVec> f, gmx_bool bAddF)
| ^~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spline_work.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spline_work.cpp
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp: In function 'void do_redist_pos_coeffs(gmx_pme_t*, const t_commrec*, gmx_bool, gmx::ArrayRef<const gmx::BasicVector<double> >, const real*)':
/<<PKGBUILDDIR>>/src/gromacs/ewald/pme_redistribute.cpp:453:6: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
453 | void do_redist_pos_coeffs(struct gmx_pme_t* pme,
| ^~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_spread.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_spread.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_pp_comm_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_pp_comm_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_coordinate_receiver_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_coordinate_receiver_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_force_sender_gpu_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_force_sender_gpu_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/ewald/pme_gpu_program_impl.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/ewald/pme_gpu_program_impl.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/calcgrid.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/calcgrid.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft5d.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft5d.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/parallel_3dfft.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/parallel_3dfft.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/fft/fft_fftw3.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/fft/fft_fftw3.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/clfftinitializer.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/clfftinitializer.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/hostallocator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/hostallocator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_utils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_utils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/gpu_utils/gpu_testutils.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/gpu_utils/gpu_testutils.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/cpuinfo.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/cpuinfo.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/detecthardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/detecthardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/gpu_hw_info.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/gpu_hw_info.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/hardwaretopology.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/hardwaretopology.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/printhardware.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/printhardware.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/hardware/identifyavx512fmaunits.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/hardware/identifyavx512fmaunits.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacymdrunoptions.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacymdrunoptions.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/legacysimulator.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/legacysimulator.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/md.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mdmodules.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mdmodules.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/mimic.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp: In member function 'void gmx::LegacySimulator::do_mimic()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:227:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
227 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:53:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:379:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
379 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:421:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
421 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
422 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
423 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
424 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
425 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
426 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:437:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
437 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
438 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
439 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
440 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
441 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:451:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
451 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
452 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
453 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
454 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:509:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
509 | dd_collect_vec(cr->dd, state, flocal, ftemp);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:519:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
519 | mimicCommunicator.sendForces(ftemp, state_global->natoms);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/mimic.cpp:533:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
533 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'void gmx::changePinningPolicy(PinnableVector*, gmx::PinningPolicy) [with PinnableVector = gmx::PaddedVector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >]':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/minimize.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp: In member function 'void gmx::LegacySimulator::do_md()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:253:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
253 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:749:49: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
749 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:753:27: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
753 | pme_loadbal_do(pme_loadbal, cr, (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
754 | fplog, mdlog, *ir, fr, state->box, state->x, wcycle, step, step_rel,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
755 | &bPMETunePrinting, simulationWork.useGpuPmePpCommunication);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:767:35: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
767 | setCurrentLambdasLocal(step, ir->fepvals, lam0, state->lambda, state->fep_state);
| ~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:810:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
810 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:815:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
815 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:918:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
918 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
919 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
920 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
921 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
922 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
923 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:945:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
945 | do_force(fplog, cr, ms, ir, awh.get(), enforcedRotation, imdSession, pull_work, step,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
946 | nrnb, wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
947 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
948 | fr, runScheduleWork, vsite, mu_tot, t, ed ? ed->getLegacyED() : nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
949 | (bNS ? GMX_FORCE_NS : 0) | force_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1100:25: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1100 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1128:45: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1128 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1136:44: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1136 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1152:40: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1152 | stateGpu->copyForcesFromGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1159:33: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1159 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1160 | observablesHistory, top_global, fr, outf, energyOutput, ekind, f,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1161 | checkpointHandler->isCheckpointingStep(), bRerunMD, bLastStep,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1162 | mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1194:55: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1194 | bIfRandomize = update_randomize_velocities(ir, step, cr, mdatoms, state->v, &upd, constr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1266:46: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1266 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1267:47: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1267 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1273:42: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1273 | stateGpu->copyForcesToGpu(ArrayRef<RVec>(f), AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1280:34: note: parameter passing for argument of type 'gmx::ArrayRef<const t_grp_tcstat>' changed in GCC 7.1
1280 | integrator->integrate(stateGpu->getForcesReadyOnDeviceEvent(
| ~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1281 | AtomLocality::Local, runScheduleWork->stepWork.useGpuFBufferOps),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1282 | ir->delta_t, true, bCalcVir, shake_vir, doTemperatureScaling,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1283 | ekind->tcstat, doParrinelloRahman, ir->nstpcouple * ir->delta_t, M);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1290:48: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1290 | stateGpu->copyVelocitiesFromGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1393:53: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1393 | stateGpu->copyCoordinatesFromGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1429:55: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1429 | stateGpu->copyCoordinatesToGpu(state->x, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1437:58: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
1437 | stateGpu->copyVelocitiesToGpu(state->v, AtomLocality::Local);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/md.cpp:1455:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
1455 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/replicaexchange.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/replicaexchange.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void write_em_traj(FILE*, const t_commrec*, gmx_mdoutf_t, gmx_bool, gmx_bool, const char*, gmx_mtop_t*, t_inputrec*, int64_t, em_state_t*, t_state*, ObservablesHistory*)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:545:31: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
545 | dd_collect_vec(cr->dd, &state->s, state->s.x, globalXRef);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void {anonymous}::EnergyEvaluator::run(em_state_t*, real*, real (*)[3], real (*)[3], int64_t, gmx_bool)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:845:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
845 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, count, nrnb, wcycle,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
846 | top, ems->s.box, ems->s.x.arrayRefWithPadding(), &ems->s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
847 | ems->f.arrayRefWithPadding(), force_vir, mdAtoms->mdatoms(), enerd, fcd, ems->s.lambda,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
848 | graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
849 | GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES | GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
850 | | (bNS ? GMX_FORCE_NS : 0),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
851 | DDBalanceRegionHandler(cr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:905:13: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
905 | sum_dhdl(enerd, ems->s.lambda, *inputrec->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = double; _Alloc = std::allocator<double>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<double>::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.h:47,
from /<<PKGBUILDDIR>>/src/gromacs/nbnxm/benchmark/bench_system.cpp:46:
/usr/include/c++/10/bits/stl_vector.h: In constructor 'gmx::BenchmarkSystem::BenchmarkSystem(int)':
/usr/include/c++/10/bits/stl_vector.h:960:18: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<double*, std::vector<double> >' changed in GCC 7.1
960 | _M_fill_insert(end(), __new_size - size(), __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/rerun.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h: In function 'bool do_em_step(const t_commrec*, t_inputrec*, t_mdatoms*, em_state_t*, real, PaddedHostVector<gmx::BasicVector<double> >*, em_state_t*, gmx::Constraints*, int64_t)':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/runner.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In function 'void init_em(FILE*, const gmx::MDLogger&, const char*, const t_commrec*, t_inputrec*, gmx::ImdSession*, pull_t*, t_state*, gmx_mtop_t*, em_state_t*, gmx_localtop_t*, t_nrnb*, t_forcerec*, t_graph**, gmx::MDAtoms*, gmx_global_stat**, gmx_vsite_t*, gmx::Constraints*, gmx_shellfc_t**)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:385:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
385 | initialize_lambdas(fplog, *ir, MASTER(cr), &(state_global->fep_state), state_global->lambda, nullptr);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:54:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/shellfc.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_lbfgs()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:1858:41: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
1858 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1859 | static_cast<real>(step), &ems.s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1860 | observablesHistory, ems.f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp: In member function 'void gmx::LegacySimulator::do_rerun()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:302:23: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
302 | initialize_lambdas(fplog, *ir, MASTER(cr), &state_global->fep_state, state_global->lambda, lam0);
| ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/awh/awh.h:69,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:52:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:551:32: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
551 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, enforcedRotation, step, ir,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
552 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
553 | state->natoms, state->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
554 | state->v.arrayRefWithPadding(), state->box, state->lambda, &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
555 | f.arrayRefWithPadding(), force_vir, mdatoms, nrnb, wcycle, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
556 | shellfc, fr, runScheduleWork, t, mu_tot, vsite, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:567:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
567 | do_force(fplog, cr, ms, ir, awh, enforcedRotation, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
568 | wcycle, &top, state->box, state->x.arrayRefWithPadding(), &state->hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
569 | f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd, state->lambda, graph,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
570 | fr, runScheduleWork, vsite, mu_tot, t, ed, GMX_FORCE_NS | force_flags,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
571 | ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:581:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
581 | do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t, ir, state,
| ~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
582 | state_global, observablesHistory, top_global, fr, outf,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
583 | energyOutput, ekind, f, isCheckpointingStep, doRerun,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | isLastStep, mdrunOptions.writeConfout, bSumEkinhOld);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/rerun.cpp:641:21: note: parameter passing for argument of type 'gmx::ArrayRef<const double>' changed in GCC 7.1
641 | sum_dhdl(enerd, state->lambda, *ir->fepvals);
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp: In function 'void relax_shell_flexcon(FILE*, const t_commrec*, const gmx_multisim_t*, gmx_bool, gmx_enfrot*, int64_t, const t_inputrec*, gmx::ImdSession*, pull_t*, gmx_bool, int, const gmx_localtop_t*, gmx::Constraints*, gmx_enerdata_t*, t_fcdata*, int, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, const real (*)[3], gmx::ArrayRef<double>, history_t*, gmx::ArrayRefWithPadding<gmx::BasicVector<double> >, real (*)[3], const t_mdatoms*, t_nrnb*, gmx_wallcycle_t, t_graph*, gmx_shellfc_t*, t_forcerec*, gmx::MdrunScheduleWorkload*, double, real*, const gmx_vsite_t*, const DDBalanceRegionHandler&)':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:936:6: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
936 | void relax_shell_flexcon(FILE* fplog,
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/utility/arrayref.h:55,
from /<<PKGBUILDDIR>>/src/gromacs/math/arrayrefwithpadding.h:49,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.h:42,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:40:
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1094:13: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1094 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, mdstep,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1095 | nrnb, wcycle, top, box, x, hist, forceWithPadding[Min], force_vir, md, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1096 | lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1097 | (bDoNS ? GMX_FORCE_NS : 0) | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/shellfc.cpp:1188:17: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
1188 | do_force(fplog, cr, ms, inputrec, nullptr, enforcedRotation, imdSession, pull_work, 1, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1189 | wcycle, top, box, posWithPadding[Try], hist, forceWithPadding[Try], force_vir, md,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1190 | enerd, fcd, lambda, graph, fr, runScheduleWork, vsite, mu_tot, t, nullptr,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1191 | shellfc_flags, ddBalanceRegionHandler);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/simulationcontext.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/simulationcontext.cpp
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrun/tpi.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_nm()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:2766:40: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
2766 | relax_shell_flexcon(fplog, cr, ms, mdrunOptions.verbose, nullptr, step, inputrec,
| ~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2767 | imdSession, pull_work, bNS, force_flags, &top, constr, enerd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2768 | fcd, state_work.s.natoms, state_work.s.x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2769 | state_work.s.v.arrayRefWithPadding(), state_work.s.box,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2770 | state_work.s.lambda, &state_work.s.hist,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2771 | state_work.f.arrayRefWithPadding(), vir, mdatoms, nrnb,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2772 | wcycle, graph, shellfc, fr, runScheduleWork, t, mu_tot,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
2773 | vsite, DDBalanceRegionHandler(nullptr));
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/handlerestart.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/handlerestart.cpp
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_cg()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp: In member function 'void gmx::LegacySimulator::do_steep()':
/<<PKGBUILDDIR>>/src/gromacs/mdrun/minimize.cpp:533:37: note: parameter passing for argument of type 'gmx::ArrayRef<gmx::BasicVector<double> >' changed in GCC 7.1
533 | mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
534 | static_cast<double>(step), &state->s, state_global,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
535 | observablesHistory, state->f);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/10/vector:72,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.h:50,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/runner.cpp:46:
/usr/include/c++/10/bits/vector.tcc: In member function 'void std::vector<_Tp, _Alloc>::_M_fill_insert(std::vector<_Tp, _Alloc>::iterator, std::vector<_Tp, _Alloc>::size_type, const value_type&) [with _Tp = gmx::BasicVector<double>; _Alloc = gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy>]':
/usr/include/c++/10/bits/vector.tcc:509:5: note: parameter passing for argument of type 'std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> >::iterator' changed in GCC 7.1
509 | vector<_Tp, _Alloc>::
| ^~~~~~~~~~~~~~~~~~~
cd /<<PKGBUILDDIR>>/build/mpich-dp/src/gromacs && /usr/bin/mpicxx.mpich -DGMX_DOUBLE=1 -DHAVE_CONFIG_H -DUSE_STD_INTTYPES_H -I/<<PKGBUILDDIR>>/build/mpich-dp/src -I/<<PKGBUILDDIR>>/src -isystem /<<PKGBUILDDIR>>/src/external/thread_mpi/include -isystem /<<PKGBUILDDIR>>/src/external -isystem /<<PKGBUILDDIR>>/src/external/tng_io/include -isystem /<<PKGBUILDDIR>>/build/mpich-dp/tng/include -isystem /<<PKGBUILDDIR>>/src/external/lmfit -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -DNDEBUG -fexcess-precision=fast -funroll-all-loops -fopenmp -std=c++14 -o CMakeFiles/libgromacs.dir/mdrunutility/logging.cpp.o -c /<<PKGBUILDDIR>>/src/gromacs/mdrunutility/logging.cpp
In file included from /usr/include/c++/10/vector:67,
from /<<PKGBUILDDIR>>/src/gromacs/commandline/filenm.h:48,
from /<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:55:
/usr/include/c++/10/bits/stl_vector.h: In member function 'void gmx::LegacySimulator::do_tpi()':
/usr/include/c++/10/bits/stl_vector.h:1338:16: note: parameter passing for argument of type '__gnu_cxx::__normal_iterator<gmx::BasicVector<double>*, std::vector<gmx::BasicVector<double>, gmx::Allocator<gmx::BasicVector<double>, gmx::HostAllocationPolicy> > >' changed in GCC 7.1
1338 | _M_fill_insert(begin() + __offset, __n, __x);
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:591:26: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
591 | nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
592 | fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:663:34: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
663 | nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
664 | -1, fr->cginfo, x, 0, nullptr);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
722 | fr->nbv->convertCoordinates(AtomLocality::NonLocal, false, x);
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:722:40: note: parameter passing for argument of type 'gmx::ArrayRef<const gmx::BasicVector<double> >' changed in GCC 7.1
/<<PKGBUILDDIR>>/src/gromacs/mdrun/tpi.cpp:745:21: note: parameter passing for argument of type 'gmx::ArrayRef<double>' changed in GCC 7.1
745 | do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
| ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
746 | wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
747 | &state_global->hist, f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
748 | state_global->